The Reformation - idea in progress

[Antagonist]

Interesting idea, I'd definately like to see some more mod projects set after the end of M2TW, a lot of scope for interesting conflicts and units.

I always find it difficult suggesting faction choices because as I play a lot of battles I always want as diverse a unit roster as possible, I'd be loathe to have two or three factions from the same culture, but if the campaign is a priority then historicity must come first.

Some thoughts on the ones you mentioned:
Byzantines - I see the argument for dropping them as they were pretty much gone by 1450, but the great symbolic significance of the fall of Constantinople seems a shame not to depict. Maybe mention it as a Historical Event or something once it happens?
Genoa - I'd advise dropping them if they're going to be very similar to other Italian states, but I suppose they were important.
Livonia and Teutons - I'd like to see them both but it's probably better to merge them.
Moscow and Novgorod - Merging is a good idea.
Ireland - Not much happening in 1450, but after 1580 or so becomes much more significant. Probably not enough to justify a faction, but it should have a significant rebel presence - a rebellion there before 1600 (with Spanish aid) came very close to ruining Elizabeth I financially and militarily. Would be interesting to play as (irregular light-armoured troops poor in pitched battle but masters of ambush and guerrilla warfare) and could work if you needed a small faction in the religious wars, but certainly not 1450.
Navarre - I like them, but again, probably not big enough in the grand scheme.

What about Switzerland? Pretty interesting in the 15th Century at least, gained independence and held a formidable military reputation for a while.

Anyway, good luck.

Antagonist