I like the idea as well, however, this would become more challenging for customer races. I still suggest the following for custom races to make them feel more unique...
1. Give one a certain number of habitation points for a star system (example 16)
2. Allow one to pick number of planets in the system.
3. Allow one to pick how to use the habitation points toward planets in that system. (see following examples)
a. Home world uses 12 habitation points (class 12 planet)
b. Second planet uses 4 habitation points (class 4 planet)
or spice it up even more....
c. Home world uses 10 habitation points (class 10 planet)
d. Second planet is extreme world uses half habitation point per class use 4 habitation points for radiation world (class 8 radiation planet)
e. Third planet is extreme world uses half habitation point per class use 2 habitation points for heavy gravity world (class 4 heavy gravity planet)
4. Then add rings/moon bonus. (example homeworld has rings no astroids in system) or you could use a point system for astroids/rings/moons even gas giants similar to the above suggestions.
5. Last your suggestion one gets (example 5) points to use for capital adjacency bonus's similar to the following...
a. +2 research points
b. +2 economy points
c. -1 military point (limit this to 1 negative points one can take off to gain extra positive adds additional twists) [see more information below]
d. +2 growth (population) points
Personally I think this would make for a very unique custom race (at least for the home world/system).
As far as negative points for adjacency this is for those who say this won't effect the game. This would prevent me from building military next to the capital as it would be almost pointless... If half your tiles are right next to the capital this can be very limiting especially if this was manufacturing/research/economy.
Please use at least some of this for the game