The Fall from Heaven 2 mod has implemented this race limited automatic unit promotion for orcs (and perhaps other units). Someone who has much more modding knowledge than I could look at that code as an example. Kael may even give you the relevant code if you ask.
As far as implementing the leaders, Fall from Heaven 2 is again a good source. That mod has unique (as in only one) units that can be built. Sort of like wonders (only one can be built for the whole game), but in unit form. That could be a way to implement the MoO2 leaders. A random event could spawn giving the race (civ) the ability to buy one of these unique units (instead of building them). To implement it exaclty as in MoO2, with varying prices depending on race picks, leaders already owned, state of game, and a limited (four slots) pool of owned or available-to-be-purchased leaders would require quite a bit of tweaking, but the FFH2 code may be a good start.
I'm not sure I follow your line of thinking completely: all races already have a 2 leader pick. What's missing for some are specific Traits and Leaderheads (some just feature as doubles).
You could define the planet (city) tiles on the map as being land and everything else as being water. Then the only way to get land units from planet to planet is with a transport.
Basically, this would mean rebuilding the entire map. I was thinking more like giving them a Paratrooper promotion, preferably combined with an Air Unit defintion with a movement range of one. (Which is how I implemented Rob-Warriors in my Civ2 trials for MOOjr.)
Hyborem of the Infernals is a non-player only civ in FFH2 that could form the basis of the Antarans. It spawns on the map after a certain wonder is built. I'm not sure how you could implement the alternate dimension as the location of the Antarans however.
Well, Nebula features as impassable terrain in Final Frontier, which could act as a separation between Normal and Alternate Space. A Space Radiation/Black Hole might be used as Dimensional Portal - to disappear upon discovery of a certain advance - preferably named "Dimensional Portal". (This would be the simpler solution, as Antares is just one Solar System in MOO2.)