Colonization could actually be fixed by updating the BGS to move populations based on economic opportunity
The population of the new systems is pretty small, though. Total pre-colonisation bubble population is 6630 billion, total post-colonisation population is 0.6 billion. The mean population of a new system is about 16,000 people, which on the scale of the bubble as a whole is tiny. [1]
Anything BGS-level which actually moved populations around would be much more likely to increase colonised system populations rather than decrease them, since there isn't really much of a "down" for them to go, while you could fill their entire current populations from a single high-population system without noticeably affecting it. (The mess it made of the pre-colonisation systems would be more impressive, I think)
However, since Frontier were pretty explicit pre-release about there not being any "upkeep" equivalent for systems (though there is the "happiness" metric to play with if you do want to build somewhere nice to live in a RP sense) I don't think it'd be practical for them to introduce anything like that in future either.
[1] The mean population of a pre-colonisation system is about 300 million, which is heavily skewed by the billion-plus ELW agricultural systems, since the
median population of a pre-colonisation system is about 200,000.
What that means is, if you imagine the game models a real human civilization - why would any people migrate to that station??
On the numeric scales involved, an appeal to "because they're really weird" actually works pretty well. It's only 1 in 10,000 people across the galaxy as a whole, and more people than that are really weird.
(But there are
so many ways in which the game's modelling of population led to bizarre conclusions if you thought about it too much, pre-Colonisation, that it just doesn't make sense as a framework to try to build anything more concrete than its current extremely abstract model on top of)
"Travel times" is also a factor, of course: you can cross the entire bubble in under an hour in a moderately fast ship. The sorts of patterns of settlement where the frontier was actually a frontier happened when the equivalent travel times might be multiple days, not an extra ten minutes on the morning commute.