I'm from MG so I can can only point out what's possible with MG:
I am planning to make what is essentially a giant scenario.
Basically the player controls the avatar of an ascendant and their goal is to protect a kingdom from a series of attacks over many thousands of years by some evil force.
Ok, sounds interesting.
Player character will be able to do any action in the game, although they will need to be trained to do them. Some functions require simply building upgrades and buildings, while in other cases the player must "learn" to do things from in game characters or "studying".
Easiest way for this is locking commands by Upgrade-requirements. At least in MG you can give upgrades to a player with Lua-code.
For the other character aspect players must increase a relationship score with other factions, I am pretty sure I can do this with "faction" resources and LUA with features I am already aware of. When they reach a certain level of relationship the other faction will teach them skills, each faction has special skills that only they use.
Yes that should be easily done with ressources and Lua, or only Lua (see red/blue box in Battleglest) -> unlocking spells like above with upgrades.
Study/Research/Learning is more complex. Essentially the player clicks the study button to open a menu and "studies" a school of magic or knowledge they already have access to. Based on some stats and their knowledge of the school they will receive a base growth in that school and then a set of small chances to learn more in that school or related ones. At certain levels of knowledge, again probably easy to simulate with the resource menu, they will gain access to new skills.
That's actually more tricky. Easy, but not so nice: doing it with upgrades... ok I agree there would be many but from coding view ist the easiest way. A real goodlooking alternative doesn't exist (as far I know)
Typical skills are magic spells, new kinds of buildings, and new summons, and also learning how to produce new units from various buildings.
yes, that should be possible without much coding.
I was thinking this should be possible with a menu system like the building popup menu as well as using and abusing the resource system, with some hidden and some visible resources.
well, MG doesn't have such popups, or cutomisable menus...

Is there anything in here which can't be done with current game features in GAE?
Well I actually don't know... sorry
I am going for a sort of Battlecry style hero system, except with no class and race limitations. And of course the methods for upgrading the hero are different and the changes to what you can build and summon aren't really the same.
I'm sorry, but I don't know BattleCry, but your system sounds interesting.
I feel like the most challenging aspect of this scenario will be making all the models and dealing with map size limitations. And also not letting the player get so strong as to conquer the whole map early, although in some cases you wouldn't want to conquer allied or neutral factions.
you can check the position of the player, warn him and kill him, if he keeps leaving the game-area he has access to.
Also, is there some way to manipulate the team color system? I was thinking it would be nice if instead of having to create 5x as many models I could use the same base model with a color scheme change to indicate a higher base quality. This would be independent of a units individual level.
You could change teamcolors using the --load-mod, like I do in BattleGlest, but it's only possible in MG, I think, because in GAE each player can/have to select his own color.
What is the maximum map size and unit count before pretty bad lag starts to set in?
I would avoid more than 250 moving units... even 200 can cause problems on weaker machines. Map size ... 512x512 works for my BattleGlest, even if I'm not using the complete area. I think basically 2048x2048 could work, too (with good computers) but I never tested this.
Be nice to have more GAE multiplayer options, currently the number of people I play multiplayer with is 0.
I don't want to annoy you but so far I know multiplayer is much more stable with MG and it supports even multiplayer-scenarios
[small]PS: a few less questions per post could be a good idea to make it easier to answer more quickly[/small]