I've been surprised that there's more to complain about with this generation's systems-all three of them, then there ever has been in the past. I don't know why that is.
360:
Cons: horribly unreliable hardware, huge external power brick that essentially doubles the size of the system, EXTREMELY LOUD (which makes it VERY hard for me to even use), terrible d-pad, horrible, restrictive DRM, making online purchases a bad idea, made by an evil corporation that was found to be an illegal monopoly, pay to play online, poor backwards compatibility, outrageous $60 price tag on new games (in the U.S.)
Pros: Right now it has the best game library, though that's meaningless as the PS3 and Wii just launched, instant messenger component is integrated across every game. Good performance for the price (though Microsoft effectively raised the price $80 in the U.S.)
PS3:
Cons: Price (Sony eliminated the cheaper system in the U.S.!) Right now the game library is small (though that's meaningless as it just launched). They only offer wireless controllers, and those have sealed batteries. Restrictive DRM, making online purchases a bad idea (apparently, I can't really find the terms for it anywhere for Sony). Maybe this one is personal preference, but I've always found Sony's first party stuff to be the weakest of any console company, outrageous $60 price tag on new games (in the U.S.), $15 extra to buy an adapter to read PS1/2 memory cards.
Pros: The most powerful current console, standard (replaceable!) hard drive (effectively gives the system more RAM), free online play, good backwards compatibility (that's even going to enhance games with a new firmware update), almost as quiet as a slim PS2, despite being the most powerful of the systems (ie, they did a great job on the design), Blu Ray gives the most space for games, and could make for a handy movie playback device in the future.
Wii:
Cons: Ancient, last-gen hardware (the X-Box 1 is more advanced in many respects). Right now the game library is small (though that's meaningless as it just launched). Wii controller may be a gimmick like the DS touch screen (useful more for casual games than what we buy a system for). Nintendo seems to be targeting casual gamers, which could mean fewer real games. Restrictive DRM, making online purchases a bad idea. Unknown if the Wii will get many great third party games, or end up like the N64 and Gamecube with mostly just first party stuff, no built-in Ethernet, no HD support.
Pros: Only "big" system with first party Nintendo games, good backwards compatibility. Wii controller could still prove useful for full games. Cheapest price (although on a price/performance basis it's a rip off compared to the PS3 and 360). Game prices haven't been jacked up like on the other systems.