When villains want to destroy the world it's usually because they don't want to live in it, but they can't stand the idea of anyone else being alive without them... Egomania writ large.
Seriously though, for a start heroes lately are flat and poorly characterised because people demand to be allowed to influence the story in 'their own way' - not realising that for all the supposed 'complexity' and 'richness' of the goodvsbad or saintly/glib/arsehole choice systems, they are still following a script laid down by someone else; all they're doing by demanding to be able to self-insert themselves into the game is severely limiting the writer's ability to characterise the protagonist.
In other media, we're always a helpless audience; the action moves ahead on rails and we can only watch as characters die, fall in love, fail or succeed in achieving their dreams etc. We see everything but can change nothing, which is an effective way of creating heavy tension (and thereby cathartis when the tension is resolved). In games we're actually a big part of moving the plot or the action forward, but the problem is that almost all games are incredibly linear: there's no real difference to the story if you're good or evil except the ending cutscene, and if you die between one plot point or the next you're prompted with 'You fail. Do it again.'
Up until lately, games have been pretty much just interactive movies: worlds designed by developers in which we can shoot/run/jump/stab/(insert appropriate verb here) to our hearts' content between cutscenes... What's happening now is that developers are trying to realise a different potential in the media of gaming; a potential to let the player experience a world for themselves, to inflict and be inflicted upon, to have their point of view and morality influenced by experiences they could never have otherwise had. The problem is that developers' ability to do this is ALWAYS going to be severely limited because to create a fluid, changing, reactional world you'd need to make EVERY NPC able to react to every possible action on the player's part, which would mean making them self-aware and intelligent... How would one do that?
On a lighter note, remember that in these types of games, the hero is YOU... Perhaps the hero isn't cool because you're not cool
