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At first I didn't really like that twist, but when i thought about it, it made a lot of sense with Terry having black hair etc.
And also that line from Superman suddenly takes on a whole new meaning.
Clark, what the hell are good villains?

I actually like the reveal. Since it connected with the "Return of the Joker" movie. The technology that the Joker used on Tim Drake is the same one that Amanda Waller used to create a new Batman. The storyline was planned out when they were making Return of the Joker.
I also liked the idea that Terry's brother Matt also is genetically Bruce's son. That means he too could be a superhero like his brother also. A new Robin maybe.
I wish Batman Beyond would comeback so they could continue this storyline. Come on Warners give us Batman Beyond.

Makes sense as Superman's microscopic vision can see DNA

I never read it like that. I assume Supes meant that he displayed the same heroic traits as Bruce Wayne's Batman.

I don't know if they ALWAYS intended that to be the case but in the Justice League 2-parter that was a part of Season 3 of Batman Beyond, there's a bit of dialogue where the League is trying to get Batman to join the Justice League full-time and the lines go:
Barta: "You'd have one-up on the old man. He never made it past part-timer."
Superman: "He wasn't what you would call a 'joiner'.
Batman: "Maybe he and I have something in common after all."
(as Batman's walking back to the Batmobile)
Superman: "More than you think, son. More than you think."
So it would seem like they were planning it at some point during the actual series.

For what it's worth, the plot of cloning a guy and then duplicating a traumatic event in his upbringing to re-create the same individual seems be have been lifted from "The Boys From Brazil" by Ira Levin. In that story (which was made into a pretty decent movie with Gregory Peck and Laurence Olivier), a group of old Nazi war criminals and younger neo-Nazis attempt the same thing with dozens of clones of Adolf Hitler all over the world. Kind of puts a sinister spin on the Batman thing, eh?

I agree I think they always wanted somehow to make terry his genetic son. I know they were going to do another movie with catwoman going the gene splicing

I think so, it might explain why they gave Terry and his brother black hair while their parents both had red hair.

What makes you think it was last minute? I mean, you don't like it that's all fine and good (though it holds pretty consistent with the sort of thing we see in the original comics), but there's really very little to suggest they just decided to do it off the cuff. For all we know they'd planned that from season one and just never got the chance to reveal it before the series was cancelled shrug they just never seem to specify one way or the other
+Charos+
"I have often laughed at weaklings
who thought themselves good because
they had no claws."

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No, it was a dumb last minute idea. I hated it. Genetic engineered. So damn stupid.