Would there be any way to implement it so that the bonuses would stack, but you'd get diminishing returns?
i.e.
Three starbases in a sector, each with the full accompaniment of (let's say) Culture modules. Each starbase would, if in separate sectors, would have a bonus of +343% (IIRC) to Influence. Here, though, the first starbase has the full +343% bonus, the second gets a 1/2 penalty (i.e. produces half the bonus), and the third produces 1/4 the bonus. The net bonus would then be 343*(1+1/2+1/4)=+600% under this method (as opposed to 343*3=+1029% under the current system).
Now, same situation, except one SB is lacking its Party Palace, and is +243, and the third is lacking both the Culture Palace and the Party Palace, and is therefore +193.
Total influence bonus: 343+243*1/2+193*1/4=+513% under this method, +779% under current system.
...actually, come to think of it, Solitair's proposal of giving SBs a finite capacity would work. Extending that further, how about the number of modules for starbases in a given sector being proportional to the number of systems (or planets) in that sector you control? (Empty sectors would get 4, enough to max out a trade base or build a culture palace. Resource mining modules wouldn't count toward the total.)