* MegaMan - Capcom. That's all I really have to say.
* Layton Series - This series is good. The only reason why I actually think it deserves to be cast as a "mishandled franchise" is because it was... well, sucked dry pretty much. I think Level 5 really made too many games too fast for this series.
* Mario Party - For the same reason as above. Hopefully Nintendo gives it a good break.
* Call of Duty - For being Call of Duty and that's it.

You can't deny the fact that the new games have made strides in quality, though. They've added in so much good to the series that it has been considered as it's own, seperate entity now. No longer is it just another Mario game.

Sonic
Final Fantasy
Duke Nukem
Resident Evil
Silent Hill
F.E.A.R
Devil May Cry
Megaman
Metroid
Tony Hawk

I don't deny they have made improvements graphically and by adding an online mode.  I think they've added improvements in quantity as well. It really just comes down to an opinion, which mine is that the steering and boosting is better in 64 and that the new pickups are op and hurt the balance of the new games.

ive always seen the mk franchise as its own entity since the original.

Aside from F.E.A.R., which I haven't played, this pretty much sums up my feelings actually.

Of course it's your own opinion. I never questioned that.

The two big ones for me are...

Silent Hill : after the original trilogy it went from bad, to worse, to just plain awful.

Command & Conquer : After EA got their hands on it they ruined what was arguably the greatest RTS series of all time that popularized the genre alongside Warcraft, Age of Empires, and Starcraft.

More recently though ...

Assassin's Creed: Started off as a fairly entertaining stealth/action hybrid with plenty of room to grow and improve, but Ubisoft turned it into their annual cash cow with each entry being more bland than the last.

More than suck dry quickly, I think they ran out of good ideas for puzzles. The stories in every Layton game are awesome, but the puzzles had become more of a chore in every entry. Everything after the second game is a joke compared to the puzzles of the very first game. Those were the challenge.

-> Excluding Layton Challenges, of course.

I just thew some out there off the back of my head, nice to have someone agree with me :) These ones stand out the most to me though..

It's sad seeing some of your favourite franchises go from what was once great, to being games that are just ok.. or even worse, mediocre at best. Some developers just seem so caught up on technology and making unnecessary changes (to freshen up their IP's) that they forget about the important aspects of the older games and what made them so compelling in the first place.

Dinosaur Planet