It was somewhat of a problem for me in that there were new factions introduced and new names given to old groups. The Vist Foundation is completely new as far as I know and the 'Sleeves' seem to be a new name for an old group, the Neo Zeon forces. The Federation is still the Federation though. Londo Bell is sort of like the special forces of the Federation that gets all the newest and fanciest toys.
As for factions from the way it was shaping up in the beginning I thought the Sleeves might be the protagonists of this series but after the massive collateral damage dished out by the Kshatriya I'm rather confident Banagher will side with Londo Bell and the Federation. That said the Federation has a knack for asshattery that is only surpassed but the Zeon's knack for asshattery so I expect there to be strife between the rank and file and the higher ups just as there always is in UC Gundam.