Ok i want to get a few things out.
First, i agree a lot with your opinion on needing a gateway for new players to learn the game. I have played so many games at this point where the entire first 3 hours is tutorial that i will have to kill someone if i'm forced to play another game that makes me click this to click that to see that is how it is done. i really like the popup idea for info tooltips since these are more easily suppressed individually and en masse. either way it is done there needs to be a checkbox to turn the tutorial parts off or on when you start the game. it should be a are you sure type popup warning asking if you are comfortable with figuring it out.
a few suggestions, currently there are a bazillion options in game generation. i love this but i would recommend taking a step to nest the option in menus and allow some simpler choices. i currently have the setting set to my preferred game style but as i try to convince a few newer players to try the game my settings are defaulted and i both have no way to get them back and no way to easily erase them for a newer player. so please have a starting selector. for example, (base game, everything, custom mix 1, custom mix 2, campaign arc #) then an options popup to let you customize it and set this as a saved mix or to use only for this game.
you have already started in ai war 1 to use mission and conflict notes such as wave warnings and alerts. i would appreciate if you work on taking this further to also keep the mission/objective logs as toggle visible message queue as well. This also could help you work on the needs for hidden info filters for locations outside of view and paly back to improving the ai itself. the current info block nesting is tedious and overlookable, so a more interactive notification log would be awesome.
an extension of this from the last 2 suggestions is please decided on either tabs on the top or categories on the side. please do not use both. So many things from options menus in games and infopedias become confusing and almost unnavigable when you cross this. nest the categories is fine but keep the orientation singular and consistent everywhere please. oddly this may be a wawy to make alien races shoud you add them different without people directly thinking about it by just flipping the menus while in the interface from tabs to rows or vice versa.
another "lesson" which may not be obvious. please make sure that zoom/scroll options are always capable of scrolling playable areas to the center of the screen. the number of game i have played with interfaces that obscure a scene or encounter that refuses to be viewed purely because they do not allow for the interface obfuscation is appalling. similairly as you learned by adding the red no command line. make sure commands can not get issued to outside the playable area. even in aiwar 1 there were times you could not locate things because of interface and or zooming issues. but there were alot of center on this commands once you realized they were there to use. but i would prefer not to have to rely on those. i have found it odd that no modern games have realized that if they limited their "viewport" they could get a better game experience by leaving the outside of the screen to interface only rather than this cover every inch of the screen garbage fps games have buried us in today.
and last as an opinion i would prefer that you include as much as possible of what aiwar has already brought to the universe of aiwar rather than reserving it all for expansions. alot of games of late have been trying to microsell content that should have been included in the base game. most notably in my opinion is civ 5 though it kinda began with homm4 ,gal civ 3, and aow3. not that i have a problem if for thematic or campaign reasons you break the game into multiple parts or downloads. but sell a complete product not just a engine that will run all this new content once you are willing to pay for it.
there are I'm sure lots of decisions on what to do with ai war as you go forward. i wish you well in your innovations and ai training courses.