If anything, AoW3 should have been MORE evolved from two sequels than E:Wom from two measly expansions.
On most major projects, a MASSIVE part of the project will be taken up by developing the game engine. Not in designing the play mechanics of the game like you are talking about, but in getting everything to render right, getting the UI to work right, and all that basic stuff.
AoW3 could obviously not inherit its engine from previous iterations of the game. It had to redo that, which was undoubtedly a relatively large percentage of the time budget for making the game. The same is undoubtedly true for the making of EWOM - Stardock's time budget for making that game had to include a lot of time that was sunk into making the basic engine go, and not on details of what the players are actually doing strategically.
However, when you release an expansion, my expectation is that there would be a relatively small amount of time spent on engine stuff (since it is largely in place - improvements might be made though), and a relatively large amount of time spent on improving the game mechanics that you are talking about.
Therefore, I completely reject the statement that you are making. I would expect FE/LH to be vastly more evolved than AoW3 because expansions give developers time to concentrate on game mechanics rather than the engine, while the base game probably had a pretty big part of the time budget spent on the base engine.
PS - I don't even like AoW3 that much - I actually prefer LH. These comparisons are just way off base IMO.