Luxury resources are supposed to be important for civil growth of you colonies, i hear you.
However when we look a bit more closely we can see that there is an abundance of strategic ressources (you would be very unlucky not to have 2 or 3 deposits in 1 system from era 1 to 3 resources). On the other hand luxury resources are mostly scarce (on about half my playthrough i don't find any neither near my starting system) [and that's playing on abundant resources (but if i remember well this setting only affect size of deposits]

WHen i play endless legends i always have 2 or 3 luxury per region and they were mostly bonus in EL, while in ES2 they are a necessity if you want to improve your systems.

On the other hand, if you manage to find the one luxury you need, by building trade company HQ/subs on it you can multiply the outputs exponentially (a system giving 2 ionic crystal base, 10 turns later i can harvest over 20 from trading companies).

In my opinion it would be better to increase the odds of finding resources in systems and decrease the amount of resources you get from trade (also adding strategic resources to trade would seem logic).

I agree that the current Luxury resource system isn't very great.

I really like the idea of spreading a luxury bonus via a trade route.  So you'd put your HQ on the resource and disseminate it via the route, giving a benefit to all the planets.

I'm not super crazy about the current level-up mechanics for systems but I don't have a suggestion ready for that.