Responses to some sections:
1.a.iv. Matchmaking and/or NAT Punchthrough
The scope and length of AI War really makes the playing community behave not like RTSes but like online ARPGs, where most people are doing their own thing in their own instances, but would still like to socialise and have the opportunity to get together. Therefore, I suggest you should consider making something analogous and call it a Lobby or Global Chat, to sit apart from Steam Overlay - essentially IRC global/party channels that players currently playing can choose to join, as well as players who are not currently playing. Forcing a matchmaking model is too high-risk, and more importantly removes the engagement of people who are currently playing.
1.d.vi. Animation
Yes please, especially with squad-based implementations and multi-part ships. Not demanding for bloom when battleships fire their beams per se, but you'll need lively units to draw in the broader crowds.
1.e.iii. Specific Areas Of Moddability
I believe the phrases "modders can create new AI-Types" and "modders cannot create completely new AI-Logic" are fundamentally contradictory. Classic's definition of AI-Types is incorrect here and easily leads to wrong assumptions as you've tried to clarify. What we were changing in Classic is the assets and materiel that the AIs have, and how much they prefer pursuing precoded tactic X. Suggest more neutral terms like "AI Personalities" to frame them in the same league as the "Human leaders" feature.
2.c. Multi-Part, But Not Modular, Ships
There are definitely still many people who like changing their ship loadouts in-game. In particular, flag-ship units like Battleships and Neinzul Combat Carriers can be made to specialise their loadout, which would strongly benefit players having flexibility.
Are you willing to consider making an interface pre-1.0, if we can successfuly "lobby" this issue? Whether this interface sits within the game or as a separate executable entitled "Ship Editor", is less of an immediate issue. However, I would clearly like a way to make, share and download designs efficiently, in a way that I switch between vanilla, my stuff, and arbitra mod. This touches on the ability to make mod-packs.
Using this, we can at least pre-generate major variants before the game, if not within the game itself.
2.a. Squads of Units
Homeworld 2, and Dawn of War. Easy. Note that meaningful squad numbers here range between 3 (HW2 scouts) and 12 (Orks). Advise try not to go beyond this unless it's drone warms (24, Homeworld 1 Drone frigate).