About stone walls: Currently you can't build Epic Stone walls, and although you can build large stone walls, what you get on the battle map is really just the small stone wall. The reason for this is that the larger walls are bugged - there is a pathfinding issue with seige towers that can really mess things up for the AI.
Building large sophisticated stone defenses certainly took a long time, but building a basic stone wall did not. Almost all Greek cities had stone walls centuries before the game period. After the Peloponnesian war the Athenians rebuilt their stone wall, which had been destroyed as part of the peace terms at the end of the war, in a very short period of time.
I'll take a look at increasing the cost of building stone walls, and maybe the time for large stone walls, but I don't think that building a small stone wall should be all that expensive in cost or time.
Zarax: I agree on the desert peltasts and infantry. I'll probably tweak the stats so they have a significant advantage in desert and scrub. As for the Greek mercs, they were not elites, but they are the best infantry available to several factions, and I don't think they should be available in the same quantity as native troops.