[baruk]

Yep, my thinking is that big flying armies with their strategic move 3 would become the next Cheesy annoying tactic, if the province take, seige and castle storm were doable in one turn.

The seige bonus for flyers I imagine derives from their ability to fly above the fort and drop heavy rocks on it, roof or not. With no roof, perhaps flyers could storm the castle without knocking the walls down, as in the HoMM games.

The seiging system in Dominions superficially resembles that of the Total War games (shogun, medieval etc.), where there is also a 2 step process to taking a castled province: taking the province, then seiging/storming the fort. The difference is that in Total War, you can attempt to storm the fort any time you want, there is no defence value to knock down first. Laying seige to the fort over several turns has the effect of causing severe attrition to the defenders inside (about 10 to 50% losses a turn), until eventually you gain control of it automatically when the defenders surrender, or when all have starved to death.

The Dominions castle seiger has it tough, comparatively, needing to breach the defense value before being allowed to storm (the order to storm, as discussed before, only being allowed to be issued the turn after the defences hit zero). The rate of defender attrition during seige is comparitively slow (1hp a turn once they pick up the disease affliction), and easily bypassed by the use of non-eating forces, which would include all commanders.
Add to this the potential for strategic magical nastiness as an effective tool against both seiging forces and un-forted provinces, and you have a recipe for blanket castle coverage as a simple, effective tactic.