My biggest issue with champions in their current state is that nemesis champions remind me a lot of Hybrids, and so playing with a champion at all is basically forcing you to have Hybrids on. The main issue with champions as I understand it is that the player basically gets a superweapon for free that can wreck AI systems on its own (though its quite a bit harder after the guard post and guardian buffs), with no counterbalance from the AI.
So what I'd like to see is a defensive counterbalance from the AI to prevent champions from running over it, then the offensive counterbalance of nemesis champions could be broken out into it's own AI plot, similar to hybrids, and balanced accordingly.
A defensive counterbalance to champions could take the form of special guard posts or system structures seeded at generation that only activate when a shadow drive equipped ship (champion) is in the same system or an adjacent system, or can only target shadow drive equipped ships. This would create a reason for the player's normal fleet to be out and active, taking care of the shadow defenses that would otherwise wreck the champion(s).
A few ideas :
Shadow Driver I-IV: Bigger, scarier version of the OMD, Mark level is the champion hull size that it's scaled against.
Hybrid Raid Engine: Raid engine that's been infested by Neinzul Astrid organisms. Works like a normal raid engine (except for only triggering off Champions), but the spawned raid consists of Neinzul Astrid nebula ships.
Astrid Viral Cluster I-IV: Works like a Neinzul Viral Cluster, only triggers off champions, spawns Neinzul Astrid nebula ships.
Hatred Generator: Renegade Dark Spire partnering with the AI to wipe out all life in the galaxy. Gains charges every second(s) a player champion is in the same system, and the spawns are AI-allied.
Inactive Shadow Golem I-IV: Sleeping version of the Ravenous Shadow. Wakes up when it detects a shadow drive equipped ship. And it's HUNGRY.
Shadow Prototype Facility I-IV: The AI wants to get into nebulas too, and has research facilities where it's constructing it's own prototype champions. Self destructs if a player champion is in the same system to release one or more nemesis champions to threat as a one time spawn.
Shadow Research Center: The AI is experimenting on shadow wormholds and the results do... strange things to shadow drives. Works like a gravity drill, but only affects ships equipped with a shadow drive.