If you are going to implement the minifactions, I think that a good way to do it would be like upgrades. Having two options of minifactions, you should choose only one, wich would make a big diference in the gameplay.
Playing with Dwarves. Their minifactions could be Iron Hills and Blue Mountains, been Erebor (the biggest realm) the core faction. Then, you do an upgrade to then be able to build the minifaction's units and structures (to me the best would be no more than 5 new units or structures per minifaction.). The iron hills are focused in siege, been able to build the best siege machines in game, and the blue mountains in meele combat (or economy, this is just an exemple). Then, the minifaction you choose would directly affect the strategy, like upogrades and new units, and etc. Of course this would require a HUGE work to implement, but in the end this could be the diference of this mod. Like, you can play Dwarves X Dwarves, but you wouldn't been battling exactly the same units you are producing, like fighting a mirror. I have a couple ideas for the minifactios, like the dwarves (already mentioned), MotW could be Dol Amroth and Rohan, Mordor could have three (Minas Morgul, harad and khand) or two (minas morgul and evil man), the goblins could have Gundabad and Moria, and so on.
What about that old idea of making Saruman the RingHero of Isengard? I didn't played yet with Isen in Beta 4.5, but if this wasn't added yet, would be for beta V?
And the library thing? Will be add?
I was thinking about the inns, and what about making a unit only recruitable at the inn? Like for dwarves some iron hills (or blue mountains) warriors, for elves some dark elves hunters or something (descendents of the ones who didn't went to Valinor, but aren't sindar, i don't remember the name) and so on.
I think that this would make the factions too similar, something that I hated from AoE. But the economic sistem, if could be implemented, with resources like gold, stone, wood and food (mabye more, if could be add), real resouces to estabilish a camp, all the factions having lumbermills, quarrys, mines and farms and trading to obtain all of those goods. This would really rock the BFME sistem, and make this mod the best mod for bfme ever!