Paper Mario: TTYD
Include a quicksave feature, mainly for the Pit of 100 Trials but other long dungeons too.
Have the 2nd Glitz Pit Ladder be significantly harder, Pit-level difficulty or better, with a hugely buffed Rawk Hawk with new moves waiting for you at the end of it.
Have every Bowser 'interlude' include a side-scrolling level and make them a bit longer and more difficult.
Allow access to 'Luigi's Adventure' if you collect all the 'Super Luigi' Books.
Really, most of my fave games lack many major flaws, so my main request would be more (preferably challenging) content. This would go for Final Fantasy X and Twilight Princess as well.