I wouldn't call them my favorite factions, but I found the Draconis Combine and Clans fascinating, because they were so alien. That fascination hasn't really changed with era.
I don't actually have a favorite faction, because I found early on that none of them actually fit my ideals as an American to get behind. Even being a 'citizen of Earth' was not much of a clarion call for Comstar, WoB, or the Republic.
That hasn't changed by era, either, though I would be more inclined to the Republic.
Effectively, pirates and mercs allow me to sample fighting for or against any single one of these, and I could shape the force to whatever ideals I wanted.