Agree with a lot of things you said.
I also want to add a couple of things ...
1) the merchant system in M2TW is really not implemented well. A lot of people complain about this too. It's really not worth it.
2) I think the whole marriage/princesses thing could be done a little better from standard ROME. There is no alliance with marriage, which use to be a big deal.
3) I like the whole city specific units (spartan units only from sparta etc). But I want to go one step further, I think there should some way to recruit various units without going through the whole mercenary thing. Perhaps a diplomatic approach where I ask my allies or a neutral faction for a unit of war elephant or silver shield pikemen for a price, obviously an expensive one, but obtainable nevertheless. When I start playing vanilla Rome, I always thought "military access" means that your allies can let you train their specific military units, but of course I was completely wrong.
I wanted to add that I think Seleucus or someone was able to barter with India and get a couple hundred war elephants that way. That would be fun.
4) On a similar topic, I have mixed feelings about mercenaries. Without any kind of cheat, mercenaries cannot be retrain, so aside from combining them, most of them are "use and refuse" types. Furthermore, there are only several worthwhile merc (cretan archers and elephants), and the rest are pretty useless.
5) Pre-battle formation should be a little better without me having to tediously change the position of every unit for every freakin battle. This alone is enough for me to do auto-resolve. I heard there are mods for this, but haven't try it out yet.