Here's a few changes I suggest for the homesystem at the very start of the game:

• Increase the homeworld initial population to (near?) max, but reduce the population growth rate. Combined with future population transfer mechanics, this would encourage rapid initial expansion but force the player to wait for the initial wave of colonists to reproduce to continue expanding.
• Since (most) races already starting with a population from a minor faction seems strange, I suggest making acquiring one an initial quest instead. Make sure an appropriate small planet (Hot for Mavros, Wet for Kalgeros, etc) is always spawned in the homesystem, then give the player a quest to colonize it. Once they do, give them 1 minor faction pop on that planet. (This would also make the starting system more reliably valuable, rather than the crapshoot it currently is.)
• Give most homeplanets a bonus +2 pop cap, or have them automatically be at max pop cap (as if the system was upgraded to max level); it feels strange that so few pops can live on their homeplanet compared to other planets.

Having minors on a separate planet is a great idea. I suspect that multiple higher species on a single planet is a rarity in the universe due to one exterminating the other (looking at you, Cravers!)

It may be that the minor addition was more of way to quickly introduce us ot the concept of multi specied factions, rather than a definitive feature. After all, without it you would depend on migration and assimilation before having some alien population.