[Archonsod]

Flying archers would certainly be illogical (how would they aim the bow and stay airborne at the same time?). As for flying mages, perhaps the effort to stay airborne affects their concentration for spells, or perhaps they're simply unwilling to risk tiring themselves out with spells while being a few hundred feet off the ground.
Alternatively, perhaps flying units are simply unwilling to place themselves in a position which puts them in line of sight (and possibly attack range) of every archer, mage and priest in the opposing army?

Not sure about immunity to trample. Presumably the trampling unit would simply wait until they land. On the other hand, a flying unit would have an easier time avoiding the unit, but then any sufficiently agile unit should be able to 'dodge' a trample in some manner (elephants for example, are not known for being nimble).

The problem with coastal movement is handling combat (should any occur) between underwater and airborne forces. Unless of course it's treat in a similar manner to sailing (i.e. the unit effectively skips the water province).