I like the idea with L-upgrades! They just have to be worth it not like on Ark atm. So increasing TT is good way I think.
But some UL-upgrades would be nice as well. Stolen Imperium will only be an option for that when it becomes accessable to anyone again. B.E. armor ist a nice idea. But dont put Dodge on it. We have enough of those armors. Speedbuff or Evade or HP or even Crit or Reload would be awesome.
Another thin that would be awesome and maybe stick some players to Cyrene: Upgradable Disciple armor. You get normal one as reward und can uprade with some missions. Mostly long-term killing missions and maybe a few speciel Items needed. Nice buff for this armor would be Skill increase. Would be nice for beginners and not to OP and unfair for those who allready finished disciple.
Actually this would be a nice thing for every planets disciple armor. But maybe Cyrene can be the first
Upgrade missions to the HK or Xent Prototype would be awesome as well to get those items closer to alternatives. Especially the eco...
edit: maybe it would be wise do do some buff we don't have yet on guns/weapons/faps. Like lifesteal on armor or gun and 50% divine chance while refurbished heart rank X heal over time is running