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To my mind, the only hitch with that theory is that in one of the Wolverine and the X-men episodes, Logan did not seem to recall Sabertooth or Weapon X at ALL.

Actually people involved in both projects said, as I recall, that yes, Hulk vs Wolverine is directly connected to Wolverine and the X-Men. Same continuity. Which SPOILER is probably why Sabretooth and (thank God) Deadpool remained alive at the end, so they could be used again.
Also, in the X-Men episode where Wolverine battles Hulk again the flashback scenes are directly taken from Hulk vs Wolverine.

Its supposed to be a loose prequel to the series. Specifically Hulk and Wolverine's encounter in that series.