Hmm... Maybe my judgement was clouded by the thought of further combat being pointless after you capped out on RUs (bought everything you wanted).
Yes, you bring up one of the "game economic" issues that existed with SC2. You could reach a power level where nothing could stop you and the game economics would essentially be shut down. The economic cycle that existed towards the end-game turned very "un-fun" and felt more like a chore than fun. The only thing you were spending RUs on was fuel and perhaps crew, and those were minimized by the quasi-space portal and the rebirth of the Shofixti.
This is something we are spending time to address. Be it early, mid, or late game the economics of the game shouldn't feel like a chore and there should always be a threat encounter that you fear or take losses to.
I don't think needless resource gain is the only aspect wherein people get fatigued by combat. If we think of SC2, combat events were somewhat random. Or perhaps best to say that the encounter potential was random and, if you couldn't (or didn't) evade contact you would enter combat. Early-game this is exciting as it can be a real challenge, or even a chance to encounter a new species or event. Late-game, however, all the questing is over, the resources are meaningless, and it is simply an interference to progress through the remainder of the game.
There are several reasons I can think of where a player may wish to avoid what feels like tedious combat. Perhaps it's best to think of in terms of "what game am I playing right now?", or perhaps "which game is it I want to be playing right now?". So if combat is a game (within the whole game, of course), and questing, exploring, base/ship management, etc. are other games (also each within the overarching game), then there are times when the player is enjoying one game and being forced to start playing another. Imagine, for example, if I am playing solitaire and every time a queen is revealed the game makes me play a quick round of checkers. Now, maybe I like checkers, and maybe winning at checkers even gives me some sort of reward that helps me in my solitaire game (ok.. this is getting stretched, but please stay with me). Even so, perhaps what I really want to play is solitaire, making me cringe every time a queen is revealed. Basically, I'm being extracted from the game in which I am currently engrossed and plunked into a different one that I have to complete before I can go back to the one I want to play in the first place.
Perhaps, as some have said, I find this tedious because I simply don't need the resources. In this case I'm being interrupted and the reward is more of a "forced farming" event, so-to-speak. But perhaps my reason is that I am almost done a quest and I am simply excited to see the end. Maybe I don't have a lot of time to play, and my accomplishments are stymied by unwanted near-random encounters. Remember that when a player is time-limited (i.e., often short sessions), enjoyment is marked by the ability to accomplish often bite-sized goals. In situations such as these, the ability to skip combat somehow is a valid consideration.
Of course, the player should not expect to be able to skip combat whenever he or she chooses. Some combat is probably necessary (i.e., un-skippable), but combat that can be skipped should not be skipped without some form of penalty. As a penalty I suggest the following: When a player is sucked into combat by a random encounter, he or she is given the choice of which ship to use in the encounter (this is the same as SC2). Once selected, the player is given the choice of moving on with the fleet while that particular ship (obviously not the flagship) keeps the encounter distracted. The encounter ends for the player, and the fleet (minus the distracting ship) moves on. The distracting ship resolves combat on its own (AI vs AI) off-screen, and - if victorious - it returns to the fleet after some period of time. During that time, it is unavailable, and unless it loses its fight, it cannot be replaced. In other words, the player can temporarily sacrifice fleet power in order to carry on with its mission. The time it takes for the ship to return to the fleet should obviously be a balance between a meaningful penalty and a handicap so severe that nobody would use it. Nevertheless, the decision to skip combat should be strategic. Can I afford to lose fleet power? Or maybe it is better to just take a few minutes and fight the encounter myself?