For me, "ascension path" means spending 1-2APs on radically changing your pops. (Admittedly psi ascension has more of a focus on empire effects, but even then, narratively it's about your pops becoming psychic.) There could be alternatives to the existing ascensions that are still effectively ascension paths. But I think the basic question is, "What if I don't want to radically change my pops? Can't I get comparable power by leaving the pops alone and upgrading something else instead?" Well, maybe, but by deliberately abstaining from some aspect of the game, you can't expect to be automatically compensated in other ways.
Governmental reforms and whatnot are interesting ideas for APs, but I don't see any reason to make them mutually exclusive with ascension paths. Why would a super-advanced government require the pops to be normies?
The only mutually exclusive "path" I can see that would be a genuine rejection of the pop-based approach would be some sort of "automation path" that reduces your dependency on pops to make resources. (For an organic empire, it could include lots of robots too, but your primary species never *becomes* the robots, they just let the robots do most of the work.) Then it would make sense to be mutually exclusive with ascension paths: your pops aren't motivated to upgrade themselves because they are already living a life of leisure, there's no need to make themselves more productive.
A shift away from pops is already in the game to a limited extent with non-habitable Megastructures, especially the Dyson Sphere and Matter Decompressor. But those are limited in that you can only build one each of them. What if Dyson Sphere and Matter Decompressor, plus other exclusive megastructures, could be built repeatedly, but on a special AP path that was mutually exclusive with bio/psi/synth ascension? Alternatively, what if the automation path led to Fallen Empire-style buildings on your colonies that produce stuff without needing pops to work them? The challenge would be to a) make it balanced and b) keep some sort of pop management in the game so it doesn't degenerate into "one pop challenge"-type meme builds.
The problem is that ascensions are mandatory im terms of pop changes. And there should be more shades od grey here.
Assimilation should be a separated option, that can be set from free assimilation (only od egalitarians) where pops are happier, but assimilation is painfully slow, yet not mandatory, through encouraged assimilation, something like current one, to the mandatory assimilation that reduce happiness, make some other bad things, but pops assimilate much quicker, yet its forbidden policy for egalitarians.
This would solve much problems, both mechanical ones and rp.
The way the game handles synth ascension from an "ethical" standpoint is pretty weird. A Glorious Synth Master Race empire is honestly one of the most sinister forces in Stellaris; even if they're "Egalitarian Xenophile", they don't really care about any sentient life other than Synth life.
Necrophaging xeno pops into your own species? That's an atrocity (albeit not as bad as outright extermination purging).
Hooking an organic up to a computer, uploading their mind, using the file to program a Synth brain and then destroying the organic? Absolutely fine. I mean the pops themselves don't like it at all, they are clearly suffering, but at an empire level, nobody cares. (To be honest, I'm not convinced the Synth is really a "copy" of the mind of the original organic, e.g. regardless of their old ethics, after "conversion" they conveniently forget all that and subscribe to Materialist ideology. Maybe the Synth just retains the memories and skills of the organic, but not their personality.) Only the Spritualist Fallen Empire is concerned enough to make an official protest.
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