I disagree - a good system is flexible, robust and balanced.
If it's strictly preferable to give ships long mission lives than to invest into the maintenance system, the system is broken.
If it's strictly preferable to make ships fuel-efficient to the point of rendering fuel logistics irrelevant, the system is broken.
Ideally, breaking the usual assumptions would be possible but not the norm - leading to higher total costs or requiring significant design concessions.
I would agree to some point here, but that also depend in what role-play you wan't to be possible. The current system at least give you the options for some machine race or something to abuse these system. Perhaps from a mathematical perspective it is way more effective to just give ships an extreme long maintenance cycle and scrap and build new ones and ignore maintenance facilities altogether... I don't know...
If it could be better balanced I would not be against it, but I don't see it as necessary to play the game and don't abuse it.
As I said before... there are many more ways to abuse the game mechanics in Aurora but you don't need to do it to get a balanced game. Aurora is as far as I understand first and foremost a role-playing platform so you do whatever you feel is best for you to get the best playing experience.
I always restrict myself and all my factions to way more restrictive rules to how things work in the game, for role-playing. As all the factions live by the same rules it is fair and balanced.
Aurora is not a game to win, it is a game to play the way you see fit.
It obviously does not mean that there should not be some sort of balance or that things can be changed or fixed.
I did state in one of my answers above that I think the resource cost for technology in and if itself is gamey... you don't pay 20% higher resource cost just because a technology is 20% more efficient or better. In the real world the cost of a tank of the same mass is going to be roughly the same no matter what technology it contains since the industrial technology to develop it is there to support it as well. Any new matriel used in the new tank is now produced by industry as new technologies has been discovers, industry that would otherwise have produced the old material for the old tanks and so forth...
So the industrial cost are going to remain roughly the same. What changes are usually the skill of labour, today the cost of labour is much more expensive since both the ones that build, operate and maintain equipment need to be more skilled. So it is often the human investment that change, you need more skilled people over time for development and research but less for actual production. Both operation and maintenance take more skilled people but often less people overall.
If the cost of stuff remains roughly the same and instead you need to advance the industry and human capital to support it to develop it things would work better in this particular regard because the cost to maintain would be roughly the same in terms of human resource invested in it. managing the skill to maintain more advanced equipment would go hand in hand with the actual advanced equipment. Old equipment would still need to be maintained and would become more and more expensive over time in comparison with new technology. This is usually how it works in real life, older system become more and more expensive to maintain as newer more efficient technologies take over.
Exactly how any of this would translate into Aurora I have no clue, but the system as it is are Gamey to begin with. I don't think there is an easy fix so using personal restriction to get the game to play like you want to is sufficient to a certain degree here and there.