I would see another model:
If you have a new species in your empire, you should get a prompt to:
a) Commit genocide and kill all of the remains of a selected species in your empire and replace it with a chosen one (this would affect diplomatic relations with other empires. Mainly with the empire that consists mostly of the species being killed)
b) Enslave the whole species (cheap workers,constructors and researchers but affects diplomatic relations)
c) Assimilate itd) Don't do anything, just administer the planet (I'll ecplain that in the last paragraph)
Once a species is assilmilated (every turn it would have a few points to the Assimilation meter iand once it reaches 100% a few options would be avialable). I'll call these options "Designations":
Designate to:
a) Research (The species stats would be used to do research). That way a player would have a reason to populate planets with that certain species.
b) Combat (With two options: Ground and Space)
c) Construction (Ships and ground infrastructure and special buildings)
d) Do nothing (No designation. No bonuses used)
The
bonuses should be empire wide. And for example if a planet is populated by species A the infrastructure and ships are constructed by Species B. Species B only does the work they are deignated to and does not count to the overall population of the planet. The bonus could be calculated based on abudance of a species B in your empire. The bonus would be added to your starting races bonus based on that calculation/algorithm.
Explanation: The Starting species is always the dominant species. The dominant species does always does the work (produces ships, infrastructure, researches), but if you have another species more skilled in some taks it slowly replaces the original species in it's work, however the starting species always coorinates and administrates the whole project (that's why there's an additional bonus to your starting speces stats).
To compensate the "Gotta catch'em all" factor there could be penalties for having to many species in the empire. This could be achived by having a "Tolerancy" option in the race picks. For example: Tolerant species can assimilate many new species in the empire without penalties. Xenophobic species, on the other hand, can assimilate fewer species and if there are to many in the empire the player starts to get some penalties to research, production, etc. That's when the "Don't do anything" (d)) option kicks in. There will be no Xenophopic reaction from the society if there's no assimilation attempt, but you can choos to assimilate if the expected bonuses are far greater to the xenophobic reaction. It's your choice. Hey, if the empire's xenophobic it can always kill them after the assimilation if you don't like them. Forget the diplomacy

You're probably at war with all your neigbours...