I don't know if you've read my last recommendations, but I hope you'll read this one.
1. You can take some inspiration from the Perfect Dark campaign on N64; the aliens offer many expansion possibilities.
2. You can also find a lot of inspiration in similar games like "Erina and the City of Machines" and "Nightmare Knight: Sacred Maiden & Fallen Magic."
3. Consider having small side quests alongside the main story with NPCs.
I hope these aren't too demanding. If I find anything else interesting, I'll let you know.