1. TP
2. OoT
3. FSA
4. TMC
5. The Oracles
6. ALttP
7. TWW
8. MM
TP had barely any flaws. The only ones I think are flaws are too many rupees and that it could be harder. The lack of sidequests was good because sidequests would take away from the main quest. One or two is fine, but not too many. This is the problem I had with MM. The cluttering of sidequests greatly took away from the main quest and made it too short. TP was awesome with everything else.
OoT is second because it, too, is awesome, but not quite as good as TP. It had great bosses and dungeons and stuff, but it had more flaws. Like an insane amount of glitches, dungeons are too short, and the like. The game is great, but it has a few more flaws than TP.
FSA was so awesome. Great gameplay, great levels, dungeons, and bosses, and great a lot of things. Just the hold-only-one-item-at-a-time thing threw me off. And that's a big flaw. The game is also rather easy.
TMC was awesome, but too short. sidequests cluttered the game, but the main quest was awesome. The dungeons were great too, even if there were only six.
The Oracle series is great, even though I've only completed a couple dungeons in both. The games are getting hard. I like story and the gameplay, but both games are just so hard, I haven't touched them in awhile.
ALttP isn't quite as great as the ones mentioned above because of it's insanely hard dungeons and other things. The dungeons were good and long, like I like them, but way too hard. Too many enemies and too many traps and stuff. That's a big flaw, plus the bosses were easy. Hard dungeons with easy bosses just doesn't sound right. Two big flaws.
TWW is waaaaay too easy and boring. Big big flaws there. The overworld is too big, the dungeons are too short and easy, the bosses too easy, and I can point out other flaws. The game is generally boring, though.
MM is the worst. Too many bad sidequests cluttering the game, the gameplay is too short, the dungeons aren't great (with the exception of the Stone Tower Temple), a really lame and easy final boss, and I could name a lot more. The game just wasn't that good.
That's my list.
