My general view is that the easiest approach would simply be seperating the campaign into 3 completely independent onces, early / high / late , thus we can remove some factions in the later periods and with this approach we'll end up with almost all factions in at least one campaign.
For example, to go for the current early campaign, I'll approach it in the matter of states that seriously existed as an independent entity in 1100.
Thus I'll axe : Timurids (too late), Lithuania (just a bunch of tribes in 1100), Teutonic Order (too many different variables , espeically with Lithaunia cut they become quite pointless.
And Add : Sweden , Abbasid , Georgia, Volga Bulgaria, Armenia . (there's still 2 free slots right now.)
And by high period (for example 1260s, the height of the Mongol Conquest and the full establishment of TO)
cut: Kwarezm (dead), Abbasid (dead), Volga Bulgaria (dead), Sicily (merged with HRE due to succession issues). Kiev ( dead) . Mongols (split). Armenia (became irrelevant), Georgia (also kinda irrelevant by now). Moors (split) (9 slot)
Add in : Teutonic order, Lithuania, Duchy of Muscovy, Bulgaria, Serbia, Golden Horde, Il-Khanate, Hasfid dynasty, Marinids.
Late period (1380, all 3 Scandinavian Crown passed to Oluf Haakonsson )
Remove: Norway (merger) Sweden (merger) Il-Khanate (disentergrated) Crusader States (virtually dead)
Add : Burgundy, Bohemia, Timurids, Khanate of Khazan
With this method, we essentially achieve a dozen more factions without going over individual limits.