It is time to get rid of them SE...

[Exodus-E]

Snip.

I won't deny that as of 5.0, SMN has mechanical/play-style issues (as well as potency ones).
But as I've stated multiple times, Egis themselves (aesthetic and concept-wise) aren't a part of its problems.
Else, how come SCH is similar in that it uses a pet to supplement healings, yet it works (relatively) fine for it?

With that out of the way, let's go through some of your points/claims there:

and it's clear the devs have repeatedly stated that they hate pets like the egis from 2.0.

Any sources for that particular claim?
Especially considering all those (recent) Q&As/interviews/etc. stating that they would finally implement proper Egi glamours for SMN in the near future.

If there has to be minor rewriting/retconning of the story

"Minor rewriting/retconning of the story", says you.
An entire entry from the encyclopaedia, artworks, 3D models and story/job questlines + side quests, says I.

As I said before, entirely unrealistic at this point (not to mention divisive for people who actually do like them).

Egis are a permanent fixture of this game's lore/setting, regardless of whether you like them or not.
Anything else regarding SMN is fair game, so long as it works with them (especially with the existence of Trances -> Demi-Primals).