The existing system is a bit inflexible and arbitrary, but it could be so much more interesting with a few simple changes.
Right now low levels get locked in with weaker resources and cannot be changed later - I understand that's by design, but it's a cheap mechanic, we can do so much better. Worse still, when taking over another system from a different player, that system is locked in using *their* development choices, not your own, which can cause problems for example if you're using Benthic Gems to cancel overcolonization penalties - the only recourse is to evacuate and recolonize.
Instead I'd rather see a system that allowed for multiple system development *plans* that include three levels each. All you'd need to do is add a header for the plans right over the three levels displayed on the system management screen, so that clicking them switched the view of the three levels displayed between plans. Players would start out with only the one plan, but earn access to others either through tech upgrades or through building systems using the primary plan and unlocking them like trade companies are unlocked now.
Complimenting this would be some form of build option that would allow the player to change a system over from a current build plan (the older one from the player or those from other empires) to a new one. It shouldn't be cheap but it's better than evacuating a system. Doesn't seem like it would be that hard to code for either since the game already keeps track of the upgrades on a per-system basis... all that's needed is a build item to change them over. Obviously it should take a large number of turns and be impossible to buy out. In fact I'd like to see the regular levels take more turns to implement as well, rather than the existing 1-2-3 you might take inspiration from fibonnaci and go with 5-8-13. Making these levels and plans take time to implement keeps them from being treated casually. You might make the plans accessible via clicking on the system level picture in the individual solar system view rather than cluttering up the normal build queue with them.
This gives players the ability to get more use out of luxuries discovered later in the game. It also allows players to have build plans that fit specific types of systems - one for industry (your shipyards), one for food (balancing out sterile systems), one that's balanced, one for approval for systems that are hard to live in without a lot of late game terraforming and anomaly reduction. Might even have one to resist invasions in systems with key resources.
You might also consider some form of ongoing cost applied to the systems using said plans in the same manner that certain laws require a payment of influence as upkeep. If the trade companies are going to turn out rather ridiculous levels of resources per turn once they are all level 10+ and have 5 or more luxury ships attached to them, this sort of cost might be a good way to eat into those resources. If I take over another empire's system, but don't have the resources to support the system development plan they've implemented, it doesn't seem like I should be getting the bonuses from that plan. This could add another aspect to trade routes and blockades as well, depriving an enemy of certain key resources causing his systems to lose their benefits.
PS - Using Benthic Gems in three system level upgrades inverts the penalty for overcolonization and turns it into a bonus (for example, +350 from Over Colonization instead of the expected -700). That could probably be combined with the Mavros law to get a full +700. That seems like it might be a bug, you might want to double check the code and make sure that those upgrades and laws which nullify the various penalties can't go any further than reducing that penalty to a zero.
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