Unfortunately the sad truth is, Sins is a bit like Supreme Commander, MASIVE amount of numbers regarding ships, and each ship has to have AI attached to each one which means many AI algorithms constantly being processed, just like supreme commander had.
now no matter what small upgrades you get with newer CPU's, and optimizations that come from the game engine itself, you will always get slowdowns at some point because quite frankly (as it has been discussed in the forum, although not as much as I would like to see) the game doesn't take advantage of the other CORE's on the CPU.
Now for the record I am not talking about full multi threading, but even if Sins could shift some work over to another thread (some games are finding ways to shift AI routines over to the other thread) it would really help performance significantly.
A snippet from paradox forum, which also have been running into CPU bottlenecks with their more heavy games such as Victoria 2 and definitely HoI3.
"It's always much harder to introduce things like multi-threading support to an existing game because nobody thought of those particular problems when algorithms were thought out, so unless you want to rewrite everything you need to look for spots that have no shared modified data and run those in parallel. This isn’t very common, however the AI in HoI works in a way that makes this doable: The AI agents do not modify any game state directly (except their own), instead they queue up any commands they want run in a lock-free queue structure which means that other threads do not have to wait and this queue is then executed in serially in order afterward. This works well because the biggest part of AI processing is deciding what to do, not actually doing it."
Of course there solution is based on their game engine; there is a very strong chance that the AI system in ironclads engine can't be adapted in such a way; however I will finish up with the topic question-
"Avoiding Mid-Late Game FPS Slow Down"
without adding large amounts of CPU speed (most people can't justify spending nearly £400 on CPU+Motherboard just to reduce the stutter this game start getting near mid to late stage, and I do emphasize REDUCE, even a £400 CPU won't get rid of the stutter on large size galaxies at late stages of the game), or the developers finds ways to take some of the strain of the game engine bottlenecking the Main CPU thread (AI and pathing routines are usually the big culprits).
The only thing the user can do to solve this for themselves, is the tried and tested method, if you get stutter than your galaxy size and/or ship fleet sizes is too high..... most users reduce the galaxy down to an even more unrealistic number....
If a 60 galaxy size system causes stutter, then come down to 50, or 40 until you find a sweet spot that matches your system capability.
I know it's horrible not having the ability to feel that the galaxy is a GALAXY because it's so small..... But there really is nothing us players can do about it unless you just put up with the stutter.
The truth is, it's down to the developers to find ways to remedy this situation, yet it is my opinion that until they start taking advantage of parallel threading (even if only small steps to begin with) this problem of stutter and lagging is ALWAYS going to plague this game series, even rebellion.
PS, it's a shame this topic is not more heavily talked about by users in the forum, because mid to late stage stutter (lag) effects everyone at some point, and the potential of Sins in scale would grow enormously if the game engine wasn't so CPU bound.... the galaxy sizes could increase two fold, three..... four even.... imagine a 280 galaxy size system with several separate fleets with each fleet having hundreds of ships a piece. SCALE!