This mod has alot of potencial I'd say.
I'm assuming the mod takes place before the wrath of the immortals, as Karameikos is descibed as a Barony, rather than an independent kingdom(Its Baron Stefan rather than King Stefan), also, Alphatia is on the surface, not the Hollow World(one of my favorite things about Mystaria was that it was two worlds in one).
Some suggestions:
Some Countries, like Heldann, and especially Alphatia, have skyship fleets. Perhaps in the third age, you can research a tech which allows you to build small skyship scouts. Then, in the final age, several different sky-warships could be built, after researching the approapriate technologies. Both Alphatia and Heldann should have strong, unique skyships(UU).
Oh, and one last thing, I posted a thread on the mystaria message board about this mod, check it out, but it seems you have already been there! LOL