AWESOME topic. This may not seem like a problem, but I tend to ignore flaws of my favorite games. It's healthy to be more objective.
Super Mario World may have pretty colors, but the environments are noticeably bare when you go back and play it today; "woah! Look at that blue sky... and nothing else." Sonic the Hedgehog, Mario's main competition, fills the entire screen with beautiful landscapes... and it came out 2 years earlier. The music is well composed, but for such a powerful system it's so SPARSE. The tinkling, tiny sounds hardly do the epicness of the game justice. SMW also single-handedly devalued the 1up. You got them so easily and so frequently that you could easily have 90+ extra lives when you finished the game. Oh, and it was also one of the easiest games in history.
A Link to the Past had a few innovations, for sure, but even the most stalwart Zelda fan must admit that Zelda II is more original. ALttP feels liks "Legend of Zelda (NES) with pretty graphics." Though you got hints on the map of where you go next, finding all the heart pieces was impossible unless you are MADE of time or you had friends that had done the work for you (or later, the internet). Some of the temples/dungeons (like Turtle Rock) are incredibly easy to get lost in. Zelda works best when it manages to strike a balance between combat and puzzles. Too many of the dungeons tilt the scales toward "puzzles" with their numerous mazes. The light and dark world concept was cool, but switching between the two could easily become a pain when you weren't sure exactly where you were supposed to use the mirror.
Symphony of the Night is set in a huge castle, which is a great concept if Alucard didn't move so #$%^ slow! Seriously, sometimes the only way you felt like you were making progress in a decent amount of time was to turn him backwards and do the backdash over and over and over and... That's NOT what that move was meant to do, but his ridiculous pace forced you to do it. The beautifully orchestrated music would abruptly stop every time you passed through a connective hallway or entered a save room. (Luckily, they realized this and corrected in the later Metroidvania titles). Also, Konami must have thought that having an annoyingly clunky, crowded, and obtuse inventory system was required just so they could call their game "an RPG." While the difficulty was pretty reasonable throughout, if you learned a couple spells or found the Crissaegrim sword the game became a cakewalk. You were basically playing on "observation mode," voiding your experience of any fun, whatsoever. And the inverted castle was probably pretty earth-shaking in 1997, but today it's just... lazy. Just make the castle bigger, man!
Wow! That was pretty cathartic.