i'm making a 9*9*9 (maybe even 10*10*10) BI-Color LED cube
Well in theory you only need 9+9+9 pins for 27 pins for direct control, and a 1280 (1260?) has more then enough even without using pins 0&1, but that is not how most cubes are driven.
What you need are external shift registers for the 9x9 (or 10x10) part, requiring only 3 arduino output pin, plus 9 (or 10) more output pins for the level drivers, for a total of 12 (or 13) Arduino pins. That could be done with even a 328 board.
Also I think cubes with odd numbers of elements have better 'artistic' capablities as you have a true center for every surface.