ehm, just because the Akatsuki are antagonists, It does not mean they are the bad guys... Technically, Konoha is an assassin-employment organization... U_U
and, for the slow lads out there, a shinobi/ninja is supposed to be like an assassin... They are mercenariness, with a certain code (like not showing their faces etc). If I believed in good and evil (which I obviously do not), I'd most certainly classify every single character in this series as evil, since they are supposed to kill for money...
So, If the question was, "who would win, the protagonists or the antagonists?", then I'd state the obvious: The antagonists. Why?
A) Nagato extinguished Konoha BY HIMSELF.
B) Do you really need a reason B? Ok, just one name: Uchiha Itachi...
C) One more name you say? Ok, Uchiha Mandara...
D) Want an other one? Uchiha Sasuke...
E) Men, you 're stubborn, aren't you? Whoever-He-Is-Tobi...
F) If you really need a reason F, I'd suggest you go see a doctor... but, just in case, Kisame.