It's a very subjective decision, but as a Lominsan/Maelstrom I would have to pick Y'shtola since imo she has the coolest abilities in the game and they would translate to Dissidia attacks very well (deflect/absorb bullets, block axe with bare hands, make clones, forcefield etc).
http://www.dannykang.net/wordpress/w...0_16.38.25.jpg
http://www.dannykang.net/wordpress/w...9_00.15.29.jpg
http://www.dannykang.net/wordpress/w...8_09.22.49.jpg
The GC leaders are all badass (Merlwyb <3) but I just don't see them as playable characters, like it would take away their prestige as our leaders or something...
Hildibrand would be awesome as a side character that comes in once in a while during the story as comic relief (like Gilgamesh has become), but I don't see him as a pickable fighter either.
*edit*
For bad guys, at this point I'd pick Nael van Darnus, but depending on when/if a new dissidia comes out, I may switch to Gaius.
If I had to pick only one (good or bad), probably Nael van Darnus as a Chaos character...
