if dooku isnt sith aswell, i guess the CIS could be more like a proto-rebel alliance, as if the saga switches sides from PT to OT. also if he is a jedi in AOTC, then the sith wont really feature in the film atall, which would make it more like a harry potter III film, almost a breather from the 'main threat' (no voldemort in HP III if you didnt know).

it would be good in ROTS when the sith show up again (in the form of palpatine) that our reaction could be 'oh those guys, for got about them' and maybe as ID speculated (i think) that 'hmm, wow, that nice old man is a sith, i knew they were the good guys really!'

jedi dooku though wouldnt that require not having jedi killer grevious? grevious could just be reduced to a backseat general if his lightsaber bits were cut off.