Why not simply scale up your storage per system you acquire? maybe 25k per planet? Or allow you to build 1 storage bin per planet or something like that? I do not know what the exact numbers should be, however the more territory you control the more resources you can store.
That basically falls under the design flaw of "if you're already doing well, let's help you win even more," which is what I'm trying to avoid.
I can see a reason to hold a lot in reserves. If you have a lot of factories you can easily burn through 600k of metal if you lose your fleet or a good part of it. I know if I ever get into a slug fest I will tap out on metal really fast. It is annoying to be at my cap and to be wasting all those resources I could be using for other things if I were not ALSO at unit caps.
AI War is a game about throughput, rather than material storage. If you're already at unit cap, why are you hitting so many resources? What are you doing? Assuming that you scouted in advanced, and continually, presumably you always have several targets in mind -- go attack one, and that will solve your excess resource problem very quickly.
The big difference between TA and this game is that in TA you essentially had unlimited units. Yes, there was a global cap, but you could set that to a very high number. The limit in TA was almost always your income because your unit cap didn't prevent you from building more units or structures.
In AI War, it is easy to reach your unit caps so you easily run into a situation to wasting resources.
If you're hitting your unit caps that easily, you're either undervaluing knowledge (and thus not having enough possible ships to build, which makes it harder to routinely hit unit caps), playing on too low a difficulty (and not losing many units, so thus hitting caps easily), or playing a very conservative game in general (constant withdrawals to repair units, etc). If you play conservatively, then mercenary space docks are the outlet for getting more stuff with that excess cash. Otherwise, this really should not be a general problem, except fairly early in the game when the caps are lower in general.
Another idea I just though of is that factories can keep running forever. New units are just put in cold storage. You can activate them when your unit cap allows. However the factory can keep burning your resources and manufacturing things for future use. I do not think this would affect game balance too much since your main fleet is still limited, although reinforcements would be available quite quickly.
All of this is trying to solve a problem that I am intentionally not trying to solve. Aka, if you have too many ships and too many resources, the LAST thing I want to do is give you more ships, or resources, or whatever. That just makes the game a runaway, a downhill slide to your inevitable victory. Yes, the game is punishing you for turtling, in essence. Mercenary space docks are the one way around that, albeit at a really poor cost-to-benefit ratio, but still better than just throwing it away. But that's about as big a concession as the game is likely to see toward that direction.
To put it another way, there's no point in Chess where you just hang around on your back rows, amassing queens and pawns until you so outnumber your opponent that you just crush them. I really,
really hate that about normal RTSes (most of all because I tend to play that way myself because it usually works so well). AI War is designed in every way to try and crush that sort of behavior, and provide a more rewarding, more strategic, play environment because of it. There is only one reason there is any storage at all, really: to account for accidental under-spending during periods where you do briefly hit your cap on units if you were intentionally building to cap before a large battle.
It would now be easy to argue about how easy it is or is not to hit caps. Please don't. The fact remains, whether you hit your cap or not, when you are at all near it you should be doing something with all those ships.