You might like E.Y.E: Divine Cybermancy
The shooting mechanics were good but nothing is intuitive, respawning enemies, and the fact that sometimes you shoot people who apparently aren't enemies put me off a bit. Also, you got bro-seff.
Matrix the game
I remember having a lot of fun with that game when it first came out and the ending is great from what I recall. Jet Li's Rise to Honor is up the same alley if you like beat 'em ups although I think it's PS2 only.
Someone had also made a mod for Duke Nukem 3D called Duke Nukem Forever that was a fun couple of hours.
I've been playing Terranigma and Ogre Battle on the SNES as just random games you might look into but I'm guessing sprites and pixels aren't your thing.
