Both of these issues will be fixed. The AI as you know is a placeholder. When the AI gets coded actually for the game I pretty sure it will do exactly what you are doing here.
Which leads to this....
Currently there is no economic penalty for that many star bases. There will be. The simple solution is to spiral up the cost of so many star bases that it begins to outweigh their economic benefit. This way you still can put as many as you like or whichever ones you feel are needed but they will begin to drain the coffer (substantially) after X amount in a given sector. A straight % of total income vrs a fixed amount would fix this really fast.
Yes, but that kind of solution seems not logical. Why on earth should a starbase cost me, say 10 when my economy makes 1000 and 100 when it does 10000 because I now have 9 oter planets absolutely unrelated to that starbase ???
This hardly fits.
It might be associated with logistic (indeed, keeping many starbases working may be a work of logistics), there might be a diminishing return on benefits (after all, they have to share the same ressources coming from a given planet ; there may be some synergy, but pure addition is a bit too much.)
On the other hand, apart from just preventing the spread of starbases, the 4 hex limit looks quite artificial ; why I could not build two starbases at a few light-days of each other is beyond me! Fixing this problem with something as artificial is not the way to go!
For my part, I think the best choice lies around logistic. I would define the cost level to maintain a starbase by something like
(base cost+distance)/logistics + k . encompassed economy size)
base cost: a base value
distance: the distance to the closest colony
logistics: the logistics level in the research
encompassed economy size: the income from all planets that are within the starbase radius
k: a fixed factor to determine (see this as the cost to manage the shuttles to and from planets : the bigger the economy, the larger this cost)
the income from a given planet should be calculated independantly from the empire settings (say like all setting at at 1/3), and modified by the number of starbases that hold the planet in their area of effect. Something like:
(m+1) * economy / (m+ number of starbases)
where m is to be determined (at 0, there is a perfect sharing between starbases, the greater, the more it overrlaps. At infinite, its like now...
A simple formula like this accounts for many factors at once, makes your distant starbases costly to maintain, makes your rich starbase more costly because busier, drain your treasury in a somewhat logical way, makes stacking starbases around planets a not so good choice (especially since less developped starbase will begin eating profits from these which are not yet fully developped), so that the 4 hexes limit is not a problem anymore.