Well lets see here, I'll just go off of your list here.
Shinobi - Excellent game. It wasn't as good as Shinobi III, but it was still a hell of alot of fun, and frustratingly hard to boot.
Wario World - It was a bit too short for my taste, but I did enjoy it while it lasted
Wario Ware - Incredible game, although I don't know if it's really a sequel of any type... it's a new game series IMO.
Zelda WW - A hell of alot of fun. Although I really would have liked a few more dungeons. Not as mind blowing as Ocarina was, but still great.
Megaman - Ugh. I'm sick of the X series and never got into the Battle Networks... I wish they'd make a 2d MM9 for me already.
Castlevania - A decent game, but it doesn't quite live up to the Castlevania name due to the atrocious level design. Future sequels may though.
TMNT - Disasters. Both the GBA and Console games just aren't fun. I would have been happier paying $40 for a port of the arcade games.
Super Mario Sunshine - I enjoyed it, but it won't be showing up on any of my best games of all time lists.
Advance Wars - The wars games always have and always will rule.
Sonic Adventure - SA1 was amazing at the time... except for a few crappy characters (BIG) it was excellent and lived up to the sonic name. The sequel was depressing though.
Metroid Fusion - Too short and too linear... but still fun. Definitely the worst of the Metroid games... but that's still better then 90% of the crap out there.
Metroid Prime - Absolutely incredible. Currently this game is my favorite game of this Generation. I've said it before and I'll say it again, one of the greates transitions from 2d to 3d ever.
Phantasy Star Online - The DC game ate up my time like no other. I still haven't gotten around to opening my XB copy though.
And here's a couple of more I'll add to the list:
Rygar - It would have been great, if the combat hadn't been so repetitive... I really got sick of fighting the same damned slug over and over and over and over and over. It was still fun though.
Contra Shattered Soldier - Hella fun. Hard as hell but doable once you learn the patterns. A game that is worthy of the Contra name (unlike the PS games)
Wizardry Tale of the Forsaken Land - Currently my favorite Wizardry game (I still haven't gotten around to playint 8). It's amazing what happens when the Japanese get their hands on the Wizardry formula. A mindblowingly good soundtrack and classic gameplay made me incredibly happy. It's only for Wizardry fans though, as many find the dungeon crawling repetitive and boring. I hope they bring the sequel to the US.
Maximo - While not technically a sequel to GnG, it certainly does the games justice. Just the right amount of difficulty made me love this game.
You sir, are a hideous hermaphroditical character which has neither the force and firmness of a man, nor the gentleness and sensibility of a woman.
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