My Top 15 favorite games of all time:
1. Chrono Trigger - Party members were a bit unbalanced. Marle was useless, Frog wasn't that great, and Robo was a physical powerhouse with shadow techniques and healing that beat any other healer by far. Also, triple techs were kind of pointless because it nearly always dealt more damage just to attack three times.
2. Final Fantasy IV - Half the characters die only to come back later in the game, sometimes twice. The final boss comes out of nowhere story-wise.
3. Final Fantasy VI - Once you get at least to characters with Ultima, you've basically won the game.
4. Super Metroid - Uhh... I'll get back to you.
5. Legend of Zelda: Link to the Past - Two bosses in a row are giant eyeballs stuck in a congealed liquid. The final boss fight was underwhelming.
6. Final Fantasy VII - Extremely convoluted. Story grinds to a halt in the middle of disc two to collect three magic rocks. Jenova (a much better villain than Mr. Mommy Issues, in my humble opinion) gets shafted with a pathetically easy last battle before Sephiroth. Many more.
7. Super Mario World - Very easy, though I wouldn't necessarily call that a flaw. Visually underwhelming, though that's to be expected for a launch title.
8. Mega Man X - The first form of Sigma had a pathetic pattern that becomes tedious quickly. And what the heck is a Kuwanger?
9. Portal - Uh... I'll get back to you.
10. Chrono Cross - Don't even get me started.
11. Mega Man 2 - That freaking third fortress boss meant that if you died you had to spend twenty minutes recharging your weapons lest you lose all of your energy tanks.
12. Metroid Zero Mission - Ridley was stupidly easy on all difficulties.
13. Silent Hill 2 - Sucky combat, weird puzzles that didn't make any sense.
14. Metroid Fusion - Game holds your hand like a five-year old.
15. Legend of Zelda: Link's Awakening - Boomerang sub-quest is almost completely mandatory to finish the game. Underwhelming final battle.
I humbly consider Super Metroid and Portal to be perfect. I don't mean that they are the best games of all time. I just mean that they have no discernible flaws. If someone points out a legitimate flaw in Super Metroid, I will admit its imperfection.
I think that length breeds flaws. You can't have a thirty hour game and not screw up somewhere. Portal and Super Metroid are both three to five hours long, and that keeps their goodness so concentrated and replayable.
You can pick up Portal or Super Metroid twice a year and always have fun with them.