The issue is two-fold:
- The influence cost of systems (whether through claims or building starbases) must be paid many times over when conquered by Automatic Star System Holistic Organisms of Lien Eradication (henceforth referred to as the ASSHOLE acronym). Examples of ASSHOLEs include the Great Khan, Grey Tempest and Engame Crises;
- The very possibility of creating claims on systems after the Great Khan has turned into successor states (for example, if you're any sort of Pacifist).
The second part is really
Fanatic Purifiers, Determined Exterminators or Devouring Swarms, for example, don't destroy ownership of the systems, and simply transfer them back and forth. You also get a free casus belli to declare war on them. I feel like they're not really a problem, and ASSHOLEs should probably work the same way.
The ASSHOLEs destroy ownership of systems, create their own, but allow getting them back at the cost of rebuilding starbases with an influence cost is bad, but debatable, and can be justified as the cost of losing systems during the crisis. One thing that happened to me was the Khan taking a system, I take it back, build a starbase and pay influence. They come back, destroy the starbase, and leave. I come back, build a starbase, and pay influence again. I agree that once a system has been claimed, either through claims or the construction of the first starbase, it should be "cored" (as provinces are in EU4, for example) and therefore you shouldn't have to pay again. At least, there should be a mechanic to that effect. But I feel like that's a design decision that has pros and cons.
However, the second issue is different. Once the Great Khan decides to die, the Successor States are suddenly considered completely different people totally unrelated to the Khan, and an actual legit nation, but also completely disregard any prior ownership of systems. You don't get any claims on those planets you colonized and that were conquered literally days ago. And if you're a pacifist, those systems you had no problem taking back 5 seconds ago are now completely impossible to take back, unless they declare war on you for some reason and you get to make claims. You may be able to jump through hoops (such as liberating the systems as independent entities and the like), but that makes absolutely no sense. The second issue seems more like an oversight and a bug than a design decision.
Costly consequences of war, as annoying and unjustified they may be, I can live with. The way it works doesn't seem to make sense, but feels like it could be justified. The impossibility of taking back your systems because of a game system technicality, however, feels problematic to me.