Are there any franchises that are considered/you would consider to be bad or boring/unappealing, yet had one game that managed to be surprisingly fun or managed to exceed expectations?

Kingdom Hearts Chain of Memories. I've tried to play all the KH games over and over again, but I always end up losing interest. Chain of Memories, though? Awesome game.

Sonic Generations.

Most modern Sonic games from my experience have been mediocre overall.

Nier. Good game with awesome music, in a series that is otherwise a blight upon mankind.

Silent Hill 1-4 if you consider all games as a whole

call of duty: black ops series (a lot of content with tons of diversity)
paper mario TTYD (the rest of the series went bad)
kid icarus uprising (not so much because the series is bad, but because I wasn't a huge fan of rail shooters)

Have you played Colors? It plays very similarly to Generations, just without the classic Sonic sections. Generations is still my favorite though. The Sonic Rush games for DS are also pretty similar, just boost Sonic in 2D.

The original Paper Mario is good. I can grant that Super's divisive as hell and I despise Sticker Star.

I've yet to play Colors, but I've hear dreally good things about it, I should check it out one day.

I also did play Rush, and yeah, Rush was a solid game, I just forgot about cause I usually think about the console Sonic games before the portable ones.

Turok 2 Seeds of Evil.  Everything after it was meh.

And dammit Wright!  As someone who is playing and loving Tales of Zesteria, your avatar is RUINING IT for me!  I am offended and demand you change it!  jk, but I do chuckle everytime I see you on here now.  =P