I would fix up Knuckles... Nowdays he's super gullible and kind of seen as a bit st00pid. Though I think his VA might have to do with a part of my opinion. I liked SA2 Knuckles a lot. He was independent and not tagging along with Sonic and Tails, etc. and was mostly doing his own thing. I would make him more SA2 styled. c: Plus, what happened to the Master Emerald?? Shouldn't he be guarding that thing?
With Shadow, once again I prefered SA2 personality. I dunno, I kinda like the whole Maria thing. Showed that Mr. Grumpy has a soft side and that Maria's words could suddenly change his role or actions in the game and make him more passionate about what he was doing. Though I don't know how I would work that into the current games, seeing how he just happened to forget all that crap that happened to him and that he doesn't want to deal with his past anymore. *shrug* Also, I think he works how for him better if he could easily work for the good or bad side depending on what he feels like.
Tails, I think he could get into more of the action instead of just being a side character that helps with technology crap. Him in SA1 was pretty good, I thought.