Let's see...

Mega Man - Probably Mega Man 6, it feels like the most phoned in entry and has one of the weakest collections of bosses in the franchise.

Mega Man X - X7 for sure, the move to 3D was not kind to this game and the awful voice acting and questionable story changes did it no favors. Of anything it's a surprise that both X8 and Command Missions were good considering how awful this game was.

The Legend of Zelda - Probably Four Swords of the entries I've played, but to be fair, that was meant to be a side game to go along with Link to the Past GBA, so it blows my mind that the game has a bare bones plot and is sort of canon. Of a more major title, while I would agree that most fans would ranks Zelda II as the winner, I actually have a soft spot for it. For me personally, I'd say Phantom Hourglass. The story is serviceable but restricting the gameplay to the stylus input caused a number of problems the most annoying being the game being way too simplistic for my taste and wonky in execution.

Super Mario Bros. - Probably Mario is Missing, an odd educational game that would have been more enjoyable if I was half my age at the time I played it, which would have been about six years old. I also have no real love for Mario Galaxy but that opinion puts me in the minority it seems.

Dragon Quest - Probably DQIX of the actual main series. Its way too grindy for my taste. The main plot is okay, but it can also be beaten with the first team you roll and you can ignore most of the game's content in order to beat if you choose which is not how I feel a game should be made.

Final Fantasy - All the Bravest will likely always be one of the worst games SE ever produced. Not counting spin-offs though, I'd say XIII is the worst entry with a game that feels way too stripped down in both gameplay and story. It still boggles my mind the development team felt this was acceptable.

Metal Gear Solid - Definitely MGS4. I know some of the fanbase is trying to switch this around and make MGSV the black sheep entry but MGS4 is pretty much when I felt the series broke Kojima. The game has a lot of problems and is way too self-indulgent for its own good.

Kingdom Hearts - Eh, probably Dream Drop Distance at the moment, though part of me really wants to say KHII.

Breath of Fire - I usually don't like dissing games I've never played but, BoFVI has a pretty bad rep regardless. It apparently was aquite the flop and was cancelled fairly early for mobile title.

Suikoden - Probably Suikoden Tactics for me. There is some good here, but the bad outweighs most of it.