[Suicide Junkie]

So, if we start with SE4, and start going nuts on the modding...

- You'd change all the system backgrounds into grasslands/desert/etc terrain. Storms would be dangerous mountains (damage), or magical dead zones (shield depletion), or whatever.
Planets would become cities. Probably to represent the capital of a province, so when you capture that, you get all of the production & bonuses.

- Ships would probably be used for commanders, while units would be the regular troops. The commanders would thus carry the troops through the warppoints and be required to move units between territories.
Designs would have to be restricted a lot, but that's ok.
One-per-vehicle of a commander component, with various base speed ability, hitpoints, attack/defense values, etc.
Similar for armor, shield, weapon.
Magical items could provide bonus move, shield regen, etc.

- There wouldn't be any defensive spell casting, and offense spells would target only one enemy at a time. Combat-wide effect spells would end up as sector-effect abilities and be on all the time. The commander would have the option of using the more obscure and powerful damage types, though.

- Summoned units...
You could potentially create a scenario where there are a set of neutral races scattered about... they would be given special techs allowing them to build unique units.
The player would then have to trade with them to get the units. Balancing the AI files so that they will build transports full of units and charge a reasonable price while not also giving away the homeworld would be a challenge.
Also, any player who has met them would be able to arrange a trade deal. If they're lucky and have troops in a nearby system, they may even be able to sneak out of enemy territory.

- The lack of resource types may be the biggest hurdle. Production is equivalent to SY rate, and money will match up with one of the resources, leaving only two magic gem types... both of which will likely be found in a majority of territories.
Adjusting the facility extraction rates way down to perhaps 10 resources per month, and scaling the dominions costs up to match could work for those two at least.

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On an alternative track, you could also stick with the SE theme, and simply restrict race design.

Take the characteristics modifiers, and severely limit the maximum change to 5% or so on most.
Then you can use the cultures settings to make big adjustments in groups as the modder sees fit. Each culture would have an advantage over some of the others, as in your race-level RPS feature.

Racial techs are optional, but you could add a restriction saying "only take this if you picked culture Y" and thus match up restricted tech with your balanced race-culture setup.