This idea might sound not so great at first, but the ultimate attacks in the game at times help in changing the tide of the battle. So why not be able to change the basic look of the attack which could be in a way, a simpler version of the dye system.
In the CGI trailers of the game we saw the High Elf female blasting her 'GREEN' Lighting at everyone and in one of the Launcher screenshots we see her sporting a 'YELLOW' lightning. Why not give players the option to customize the look of their 'Overload' Ultimate, like spraying RED lightning instead of BLUE. And DK's can have an ultimate where the Flame is Blue in color instead of the regular Orange.
Obviously there should be a limitation in the selection of color and they should definitely avoid the lame colors or any other color which could prove advantageous to a player.
Doing so can again provide another layer of uniqueness to the character a player creates and i doubt it should be much of an effort.