We aren't talking about Mario here, we're talking about Megaman.
If anything has suffered during the '3D era', it was the Megaman franchise. Megaman Legends was a disaster. Megaman Legends 2 wasn't much better.
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He doesn't even wear his helmet in these games, WTF?!!?! They went on to make the god-awful Battle Network series (of which there are 20 titles, according to wikipedia). That's right... TWENTY Battle Network games.
Thankfully, Capcom came to their senses and released several awesome 2D Megaman games in recent years: The 'Zero' series and 'ZX', and I can't fail to mention the entirely AWESOME 'Megaman X' series. Megaman + Hadouken = Effin' sweet.
But now Capcom is doing one of the coolest things I've seen any video game company do in a LONG time. OMG, I'm so giddy as I write this....The newest game in the Mega Man franchise, to be released in September of this year (2008) is.... *drumroll*
Ladies and Gentlemen.... I introduce to you.... MEGA MAN 9!!

What's this? Is it some mistake? Didn't I say this was a 'NEW' game? YES! It IS new. Capcom is releasing an ENTIRELY NEW 8-BIT MEGAMAN GAME. HOLY SWEET MARMALADE!! (?)
Check it out, here's the trailer:
Did you notice that it said "In the year 20xx"? I love it.
screens:






These screens are taken from http://wii.ign.com/objects/142/14260822.html