Best V.A.T.S. (Fallout 3)
There was a general feeling of nervousness across the internet when Bethesda announced that their follow-up in the Fallout series would be an FPS. The series was known for its turn-based gameplay, not for fast-paced action. So how was Bethesda going to reconcile the two styles? V.A.T.S. was the answer. The solution was pretty brilliant if you wanted to play the game as a standard run-'n-gun FPS, you absolutely could. But if you wanted it to be more in the style of old-school Fallout, VATS would allow you to freeze the game and select the body part you wished to shoot at/hit (along with your chances of hitting said body part), nicely mixing real time shooting and turn-based RPG elements.
Purists cried bloody murder, but the gimmick worked wonders, helping set it apart from other FPS's and giving Bethesda their own unique stamp on the series. Having the ability to run right up to a super mutant, freeze time to aim a rocket launcher at its face, and blow away its face in the most horrifying way possible was and still is a pretty sweet feeling. Blowing up mutant heads being awesome
that never changes either.
Worst Two Games Essentially The Same (Pokemon Red/Blue)
Pokemon came out the gate as a bonafide blockbuster huge sales, huge exposure, and best of all for Nintendo's accounting department they were able to sell the same game twice. Pokemon introduced a new concept into the mainstream different versions of the same game. Sure, games before had used the same engine as another game, even much of the same gameplay but this was the first big example of a game selling the exact same game twice, with only a few minor differences between the two. And best of all? The catchphrase for the game was "Gotta catch 'em all!" And the only way to catch 'em all was to have both games.
This forced you to trade with friends to get all the Pokemon (or, if you didn't have any friends with the particular version you needed, to buy it yourself), given that was the only major difference between the games. The one notable example of this gimmick being used for good instead of evil would be the Legend of Zelda Oracle games. While similar, the two games told different stories, had different worlds, and different enough gameplay to justify the existence of each. The Pokemon games were not so generous, and little brothers across the country still remember the sting of being tricked into trading away all of their version's unique Pokemon for Pidgeys.