Will just add my own 2 cents here,
I love the storm system, its annoying, but in a good way. Makes a long trip more than just A+SHIFT.
On CR,
Im not sure what "end game" really is, this is an endless sandbox that you cant win... you can just bloat and bloat and bloat, i think by the time you have a full fleet of capital ships... you won the game.
Without Nexerlion to literally conquer everyone... at a certain point you just need to take a deep breath and...
Spoiler
AND
So complaining about CR not scaling up to these levels seem somewhat absurd to me.
Judging by the vanilla XP scale, game is just not design/balanced for that type of endgame, it just basically lets you decide when you hit your "Ive won already" state of mind.
That in mind, i love the CR system.
It forces prolonged conflicts to end, i personally only have problems with this MY mid game, because what i consider my end-game is a highly specialized smallish fleet that can make short work of most opponents in a relative short time. Neither me nor enemy fleets run out of CR.
Game-design-wise, you just HAVE to have some kind of "fail-safe" system to break stale-mates. Especially in a game where you encourage modding.