I agree that, as a shapeshifter, Jenova cannot (reliably) be considered a "she." I don't think it's stuck in the form of a Cetra though. Jenova Synthesis, which is just crafted from the Jenova cells that Sephiroth gathered after rebuilding his body, still maintains the "feminine" traits. It might just look like that.
Also, I feel like it was cheap that he just popped right back up after that. It would make more sense that you don't find Cait Sith number 2 until after the crater when you are in Junon and he helps get you out.
What's that?stupid Inspire thing.
By utilizing his special ability, “Inspire”, he is able to cause inorganic things to emit life; his “child”, the “cat”-shaped robot, Cait Sith can be controlled from a great distance.
Nanaki got an entire sidequest and some good character development in Cosmo Canyon during his return, his trek through the Gi cave, and his discovery of the truth about his father. Plus his relationship with Bugenhagen and his past with Hojo. He and Vincent are always in my party when I fight Hojo. I'm sure the remake will expand all of that, plus Cait's character and background as well.
After replaying FFVII earlier this year, I was taken aback by just how badly timed Cait Sith's return is. I mean, Sephiroth shows up, Cloud gives the Black Materia away and starts attacking Aerith, and then Cait Sith comes in like a goddamn Looney Tune. "Oops! Looks like I came at a bad time *hee-yuk.*"
I actually would make "Inspire" have more of an explanation in-universe. Maybe it's an ability that the Ancients used to have. Maybe Reeve's has heavy Cetra ancestry and "Inspire" was a special ability even rare among them.