I second Bayonetta 2 being better than 1.

Both are fantastic games, but 2 dialled the glorious insanity up a notch and had more colourful and appealing art design.

I actually would second the DKC bit. I like DKC1 better than 2 or 3. 

The atmosphere, level environments, and being able to actually play as Donkey Kong is just better in my book, I've never been able to make it through all of DKC2. 

And yeah as someone else mentioned the first Yoshi's Island is the best Yoshi platformer still. 

Mega Man X. X4 comes close, but in retrospect you can see it as where the series' story started getting a bit too convoluted for its own good, whereas X1's story strikes the perfect balance of being only there as much as the game needs it to be, while still coming across as more complex and mature than the original Mega Man games.

This was a good one. 

Ill go with a weird one and put kid icarus in there. I know the game wasnt mindblowing but i think we can safely say its better than the other two. I know uprising has its fans and it maybe isnt a fair comparison seeing as the games are so different, but that one kind of came and went whereas the first one still seems to have a lasting impact, and is the game people always think of when the franchise is brought up. 

Damn good pick.  It is one of my favorites, and tooie was good but too big or something.  It didnt click like the original.

I would add dead space to the list, the first just had the best atmosphere and originality.

Deus Ex /thread

Well, it depends on what you value. If it's innovation, the first game is going to be the best in most cases of successful, well-received franchises. After all, it's not nearly as hard making something better as it is making something at all.

Resident Evil (someone mentioned the remake, I'm talking OG 1996)
Dino Crisis
Yoshi's Island (already mentioned)
Donkey Kong Country (already mentioned)

My biggest favorite series/games: Wing Commander, Phantasy Star and Monkey Island.

Also Populous, Lemmings, Max Payne, Mean Streets (Tex Murphy series), Myst.

I would add Resistance: Fall of Man to the conversation.

The first game truly stands out. It has a lengthy 30 mission campaign that can be played singleplayer or local two player co-op. It had online multiplayer matches up to 40 people. It was the first game to show what the then new PlayStation Network was capable of online. Also the mood is one of a kind with its mix of WWII and sci-fi horror flavored FPS action. The sequels feel like a different IP. The American setting is not as interesting as England. Those campaigns lacked co-op and they abandoned Nathan Hale as an interesting protagonist.