I don't hate it. Confusing and makes no sense. But no hate.

Watching the Alternative Factor and I can see why most fans hate this episode indeed x'D

Glad to hear it's working out for you!

Just an update for everyone and anyone else who may read this in the future with similar concerns:
I've made headway and got through another batch, episodes 11 through 22, and I have to say I've liked most episodes, some quite a lot! Episode 22, "Space Seed" was an excellent episode, and I can't wait to see more augment stories in TOS (unless they just pick that up in Star Trek 2?), as I really read into the eugenics wars when I saw the augments in Enterprise and loved that lore.
I think the main thing that has changed is my connection to the characters, as it really took 10 or 12 episodes until I started connecting with them. Normally, at least with the other ST series', I connect with the crew after only a few episodes, but there were some inconsistencies with the early episodes which I guess was the actors and writers settling into the roles and defining their characters in a new universe, while the other series' had an established universe to work from.
I'm really loving the relationship between Bones and Spock, cracks me up every time, so they're probably my favourite crew members so far, and even the budding friendship between Jim and Spock is great to watch develop. I actually bet if I rewatch the earlier episodes with this crew connection established, I'll enjoy them more.
I'm really looking forward to the rest of the episodes as each one goes by, and yes, I feel I get the odd average episode every so often, and am prepared for the duds you have mentioned, but at the same time looking forward to the episodes I've heard talked about for many years!
So if you're reading this and in a similar situation to me, stick with it, at least for Season 1, it gets much better!

It's a different show from a different time with a different emphasis.
It's up to you, but it sounds like you really don't get it.

You must do what you feel is right, of course.
(Is making this post in compliance with IMDB's terms and conditions? Is this a copyrighted quote? Am I impersonating Obi-Wan Kenobi? Landru, HELP ME, HELP ME, HELP ME!)

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I don't mind Q type episodes in general, but at that early point if felt like too much God or mind control episodes.
Made some more headway and just finished Space Seed, excellent episode, and I've liked most of the previous episodes between 11-22.

If you don't like the episodes where Kirk has to deal with a Q-like being, skip The Squire of Gothos.
Once, a guy was borrowing my collection one DVD at a time. After watching the Alternative Factor, he quit borrowing them. You might want to skip that one, too.

I hope you enjoy it enough to stick with it; there are some real gems later in Season One, a few oddballs, and only one genuine turkey.
I'm surprised you didn't mention "The Naked Time" (episode 07,) which is one of the best Season One episodes, and, along with "The Corbomite Maneuver," a good introduction to the crew and the milieu.

While awaiting replies, I managed to fit 4 more episodes in (7-10).
I must say these felt a lot better than the others so far, besides Enemy Within of course.
I really like 'What Are Little Girls Made Of?' & 'The Corbomite Maneuver', they felt just as unique and entertaining as 'The Enemy Within'. 'Dagger of the Mind' was also good, though not as the previous 3 I mentioned, and 'Miri'was the weakest of the 4, but still not bad at all.
Thanks for the replies so far

http://www.planetplatypus.com/wp-content/uploads/2014/09/GQ1b.jpg
Luke Skywalker, your Mom was hawt!
Darth Vader

Yes, give up.

I never felt that with TNG in the same way. I actually think TNG is often rated more highly than it should be, because most of the actors imbued so much character into their parts, that the script didn't really give them. Sure, there were lots of melodramatic episodes that 'technically' expanded the characters, but it never resonated the way characters do in TOS.
Personally, I think TNG is rated higher because, production-wise, it looks better (even if I don't care for the ship, and all the pastels, and the uniforms), and there are a lot more techniques that TNG uses that bridge the divide to the way TV is presented today, as opposed to TOS, being a product of the 60s and the older studio system.'
That being said, however, TNG was saved past its first two seasons by the legacy established by TOS. If TOS hadn't existed, along with the first four feature films, TNG would never have been picked up. The pilot is awful, arguably the worst of the entire franchise (and I don't include the Animated Series), and I just can't see any network buying it if Star Trek weren't a household name and cult phenomenon back then.
DS9 never worked for me
DS9 is a soap opera in space. I give Ron Moore a lot of credit; he took a lot of risks, and generally speaking the series was rather good. He takes a lot of departures, but I think he took a few too many, even if I liked them. I try to encourage risk taking, because there doesn't seem to be too much of that in Hollywood these days (especially with movies). However, my main beefs with DS9 is that it is a soap opera, so you have a lot of silly scenes where two characters are talking about feelings, and how the relationships are going, and it just didn't feel right, not simply because you have males talking about relationships like this (because I don't care if it is the 24th Century, men just don't do that), but because the words Star Trek are on the top of the marquee. I want more exploration, and they did do that, but it ended up taking a bit of a backseat to Bajor's problems and the Dominion situation. Also, if you notice, there are only three humans in the main cast: Sisko, Bashir, and O'Brien. Keiko, Cassidy and Jake don't count as main cast members. Again, it's a risk, but this comes with a drawback especially if you're trying to attract new viewers; too many aliens tends to make too many "special" people. I love Quark and Odo, and I like Dax, but then you throw in Worf and we have too many "alien" issues to deal with. And as much as I love Dukat and Weyoun, again it's presented as a soap opera and it's just not for me.

You make some good points. Despite the episodic nature of TV at the time (hit the reset button ready for next week), there were still a lot of great character moments, especially with the main three. You really get a feel for the characters, even the non-main regulars.
I never felt that with TNG in the same way. I actually think TNG is often rated more highly than it should be, because most of the actors imbued so much character into their parts, that the script didn't really give them. Sure, there were lots of melodramatic episodes that 'technically' expanded the characters, but it never resonated the way characters do in TOS.
DS9 never worked for me, and Enterprise well, I enjoyed but after recently binge watching them again, I realised there's so little that you actually ever feel about the characters (or learn for that matter). I think of the new series, Voyager actually fared the best, despite having some of the sillier episodes, it also had some of the best, and regardless of 'sex appeal' 7of9 really added some interesting character stuff in there, once she was introduced.

Only if you want to keep going. But it also depends on what you're looking for out of this show. If you're looking for action and excitement, or some sort of spectacle, Star Trek TOS has a few of that, but in general one of the reasons why Star Trek was so good and made it into a cult-phenomenon was because these stories were about people. Because they were limited in what they could present, they were forced to keep things on a rather personal level with the characters; for this reason TOS resonated with fans far stronger than it did with TNG, VOY, and ENT (DS9 had stronger characters and interaction, but had some things going against it, some of which were out of anyone's control).
Let's take The Man Trap, for instance. The Enterprise approaches a planet where Dr. McCoy knows a woman he once had a personal relationship with. This is important because that detail likely would not have been put in there in TNG or ENT. Not that they didn't do personal character episodes, but here in TOS it was prominent, and important. Can McCoy save the life of Jim Kirk in spite of his emotions for the memories of a woman who the creature is using against him?
What Are Little Girls Made Of is another one, and it's in the first season. We have Nurse Chapel who knows a prominent scientist on a planet who was thought lost, and now she's put into a position where she may have to choose between her duty to her Captain and the love she had for Dr. Corby.
More than all this, is the little things that happen in the show throughout the series thanks to some very good direction. The greatest episode of the Star Trek Franchise of all time is The Doomsday Machine. Pay close attention to the guys in the background on the ship. The director did this intentionally to convey pathos to the audience. This opens up the Star Trek universe in a very personal and relatable way; we see these ordinary officers and crewmen reacting to the situation on the bridge and on the other ship, and it adds tension and creates an emotional connection we don't really get from much of the rest of the franchise for various reasons. Commodore Decker, played brilliantly by William Windom, is another example of how pathos is delivered; the man watched as his crew was brutally killed off by the Planet Killer, and he's overwrought by it, as anyone with a conscience would be. We often don't have scenes in much of the rest of the franchise where characters break down emotionally like this.
This is what I mean by resonating with people. That the people in TOS seem more real than the ones in the rest of the franchise, for all sorts of reasons.

The best episodes are those that are real dramas (which was the series' original intent). That doesn't mean they can't have some fisticuffs or bing-bang-booms. But it does mean that the story
isn't
merely about getting the characters into and out of trouble.
"Spock's Brain" could have been a superior episode if the writer had found some strong dramatic element to give depth to the story.

For some people, Star Trek is no good simply because there are no dragons or wizards, and nobody is wearing chain mail.
I feel sorry for them.

If you don't like season one, chances are good that you won't like the rest of the show. With that said, the best of season one is yet to come. If you don't like Balance of Terror or The Galileo Seven or Arena, then maybe the show isn't for you.
There isn't much continuity in TOS from episode to episode, so another option would be to pick and choose those episodes that fans recommend.

Stay thru season 2 ..you'll be pleasantly surprised at good those episodes are.

Check out "Balance of Terror", and then skip to some episodes from around the end of season 1 (EXCEPT "The Alternative Factor"). You can work your way back and find a number of good ones. Moving forward, in S2 try "Amok Time", "Mirror, Mirror", and "The Doomsday Machine". This should give you a better footing.

At least complete Season Two which is generally awesome.
Send her to the snakes!