I thought that the way the zero suit was handled gameplay-wise was pretty brilliant. The whole idea of losing your power suit after firing a hyper beam is really cool. Your character completely changes at that point.
My only issue is the design. I'm not really into the whole sexy video game character thing, but I'd be lying if I said they didn't do a good job with Samus' model. My problem with it is just that it's so obviously fan-service. I'm fine with calling it a necessary evil, I guess. :P
It would have been cool to see other suits appear though. Even just as color-swap options, there's the fusion suit, light suit, dark suit, and so on. When you made Samus black, she kind of looked like Dark Samus, if I remember correctly. Hopefully we'll see more of this the next time around.
The zero suit is a specific skin suit coded with her DNA. When she calls upon the power suit, it removes any boundaries between her skin and where the suit would be. It was detailed in the origin book where, in a quick moment where Samus was wearing a fairly elaborate outfit, she materialised her arm cannon to the shoulder to shoot at a creature before recalling the suit and it was revealed that all the clothing on her arm to her shoulder had been shredded by the suit materialising.
Basically, the zero suit prevents her from being stark naked while using the power suit.
As for Zero Suit Samus in the actual games, you can't count Metroid 1, though I will count Zero Mission, however, that was not so much combat as fleeing and sneaking.
Yes, the beam rendering you powerless is a nice mechanic, but not exactly fitting for how the suit works, though if I'm gonna nitpic continuity errors in the smash bros games, I'm gonna start with the MOTHER characters... --- "Nonsense, Bagan cannot be defeated". - Aliens: Super Godzilla Kool Frostbyte - XBL gamer tag.