Chrono Trigger
SNES:
The original translation was cheesy at times "...Sir Slush". Although some fights are difficult the first time through (Magus), it's pretty easy most of the time. While I'm glad you're never really required to go around grinding, some more strategy-heavy battles would have been nice. Also, why is this not on the virtual console?
PS1:
Some nice extras, but the load times are horrendous for some reason, and the anime cut scenes feel tacked on and generally break the flow of the game. Easily the worst version of the game.
NDS:
Better script (although the nostalgic part of me misses the cheesyness I grew to love...). Includes all the extras from the PS1 version, but you have an option to turn off the anime cut scenes, and the load times are as good as the SNES version. Probably the best version of the game. However, the new extras aren't exactly great. The battle mini game is boring and one of the new areas is the worst fetch quest I have ever, ever gone through.
Portal
My problem was with a single puzzle. At one point, you need to re-direct a missile into a cube of tubes so you can stand on a cube and get into a large vent. Unless I missed something, the game never hints that the tubes are destructible, and I eventually made the jump without the cube. I only found out about a year later that there was an easier solution.
Shadow of the Colossus
The controls. The camera is especially difficult to control, but from what I've played, everything could have used a little more polish. When Ueda said that the reason SotC didn't sell well was that it wasn't good enough, I can see where he's coming from. Anyone could have rented it, put the game down because of the sluggish controls, and never gotten into it enough to realize that, despite its problems, this is still one of the greatest games ever made.
The Legend of Zelda: Wind Waker
Despite the huge world, this game can feel kind of small. There's not really enough incentive to explore the many, many optional islands--other than sailing the seas and soaking in the adventurous atmosphere.
Super Mario World
Why so few power-ups? I understand a lot of time was probably spent on Yoshi's versatility, but they could have thrown in a few more suits. Limiting Mario to a small chain of islands definitely helped make the world feel more consistent, but it also felt like it lacked variety...there were only a handful of level "types", whereas Mario 3--which, due to each map being radically different, felt a little inconsistent--had a ton of variety.