What parts of the franchise are worth keeping and what parts aren't?

Concepts, story arcs, antagonists, characters, skillsets, etc.

If you could trim the fat from the franchise, what would you keep?

I loved sisters arc as most people do, but I don't really care about any of accelerator's wing upgrades. Transcendents are a miss. Magic gods beyond othinus are meh. Aleister as an antagonist was great up until the golden dawn stuff and his backstory reveal and waifuization...

You get the gist. No need for continuity; just pick and choose