Thanks a LOt, man, I wouldnt know where to start if left on my own!
Most important of all: back up everything first!
Yeah!, I already found out why.
EDIT: It could possibly be argued either way as to whether conquered people would fight for their conquerors using their own traditional styles, or even if the conqueror would want them to. History provides examples both for and against. What I personally would do would be to only allow the more common units to be built, leaving out any elite or prestige units, for example allow Hastati but not Princeps or Triarii, Legionaires but not Praetorians or Urban Cohorts, etc. This allows factions to keep some individuality and also cuts down on the amount of work. By removing the higher end units, it also allows you to move the 'merc' troops up a building level or two, so that Hastati require the Legion Barracks instead of the Militia Barracks for example.
The idea is to make the "general" units available to build, but to make available "elite unis" as mercs with a really low frequency.

I also thought that similarity in weapons would have some influence. Ie its easier to recriuit triarii in greece than in Spain, because spain traditionally used swords better than spears. So I might make triarii buildable/available for greece but not for spain.

Not too convinced about that last thing yet tho....