1. Pagans could be made to, as they did in real history, be more capable of survival than they are in CKII at the moment. It was almost heartbreaking in my current game as the 1122 Catholic Gryfs of Pommerania to see Lithuania and Finland almost completely obliterated within about five years. As it currently stands, it's unrealistic and the land just serves as a super easy land grab for anyone who borders them. I think removing Holy Wars against European pagans might do the trick, and instead make the player/AI have to work to be able to take the land. I'd still be in favor of an expanded timeline, but with the right mechanics it wouldn't be a complete necessity. Heck, I don't typically play with it but CK2+ has European Pagans that have a shot at survival. I'd like to think PI could do an ever finer job.
2. Now, I know you can twist this other ways... but ultimately, how is "Legacy of Rome" anything BUT Orthodox/ERE content? Yes, they were a Republic at one point too, but that's not the first thing regarding Rome one thinks about when they're brought up. Not only that, but would "Legacy of Rome" really be the title you'd go with for an expansion that focuses on merchant republics? Yeah, there's a certain connection, but it hardly strikes me as a logical way to market Republic DLC. I don't go "Legacy of Rome... OMG, VENICE IS A REPUBLIC LIKE ROME WAS A LONG TIME AGO SO VENIIIIIIIIIIIIICE!!!" It's going, in some way, to deal with the ERE. With any luck it'll include with it tweaks for overall Orthodox gameplay and perhaps some internal strife mechanics to keep the big blobs in line.
That, and Republics are an even smaller part of the game world than Pagans, even excluding the Mongols. You have Venice, Genoa, a county in Ireland, and I think a couple more Italian counties, and I think that's it. I'd like to see them playable some day, but on their own they're an absolutely tiny piece of the game world (and, like the Pagans, I've often seen them get stomped by the HRE). They'd need to be included with some over-arching economy mechanic overhauls, I think. And, again, when I think "Legacy of Rome", creating a trading empire ala The Hansa in EUIII isn't what comes to my mind. Both of those would be fun, Pagans and Republics (and maybe someday theocracies, but they're even less significant than Republics in the timeline of CKII). Personally, being able to play a Pagan and try to carve out my own piece of the world while holding off the Christians sounds like amazing good fun times, and it was when I've played with em'... just empty due to lack of unique Pagan stuff. Though I'd welcome Republics if only because it'd likely mean an overhaul to the economics of the game. But playing as Venice or Genoa and just focusing on building a super trade network sounds incredibly boring next to leading the barbarians of Lettigalia in glory against the Christian invaders.