So for the houses I was thinking at 3 very small variants of the main race, the empire which will be neutral. There is going to be another Space Master race to handle the research and map creation situated probably off the map, maybe in the galaxy core.
So for instace one family coming from hot regions so could colonize slightly hotter planets but not colder ones (remember no terraforming or super slow). Some may be more industrialized other more big family oriented. Always within reasonable limits (10-20%).
Benefits:
Possibility of differentiate pictures
Small gameplay and strategy differences
Easy to identify population on multiple worlds after conquests etc.
Dangers:
If not properly balanced a race may be more strong than the others
Manual diplomacy through SM as dynamic could be too influenced by the different race buffs (too much control from myself)
Thoughts?
Assuming all races are humans, I think varying the species tolerances will be good for flavor but not do a lot in terms of colonization, just because it's fairly rare to see a planet which becomes significantly easier or harder to colonize based on a 10-20 degree temperature difference - not impossible, just rare in my experience. Usually a CC 2.00 world has not only a temperature variation but also dangerous or not breathable atmosphere, no water, etc. so very rarely is there a world where a slight shift in temperature tolerance brings it from 2.00 to habitable.
I also wouldn't really vary the starting infrastructure very much, mainly because most of those facilities are necessary - there's no really different game strategy that says I want more factories and less mines, or more research labs and fewer academies. In fact, generally if I felt one of those was lacking I would build as fast as I could until I had what I needed. So you're less likely to encourage each family towards a different strategy this way, and more likely to force each one to build to cover a weakness immediately.
My approach would be to allow the randomness of mineral generation to do most of the work. Using Sol as an example, one family might get lucky and generate great reserves on Mars, thus a big mining colony is needed, while another family might find the best reserves are in comets or asteroids, thus more automines or orbital miners are preferred. This plus variation on the flavor level (e.g. choice of weapons, colonization doctrine, etc.) will set the families apart enough to make things interesting. That is to say, the situation a family finds themselves in will influence their choice of strategy much more naturally than trying to force it by tweaking species or starting factories. It is not necessary to take a Starcraft-like approach of every race being completely unique, a more Age of Empires-like approach where each race is quite similar aside from unique defining features will be more than sufficient. Of course - all only in my opinion!
As far as balance, it will never be perfect but with three players an interesting dynamic occurs where if one player is too strong, the other two will work together (to a limited degree, always looking for the opportunity to gain an edge on their "ally"...) to keep the one player from dominating. This will be interesting as long as it is not too static, i.e. the #1 power is always #1 and the #2 and #3 can only hope to contain them, rather than dreaming to surpass them...