Big D:
That's the point - Sephiroth was joining with the Planet, gaining incomparable powers over a period of years - Jenova can't do that; she's not of that world, so her own 'spirit energy' would be incompatible with the Lifestream. Notice that she doesn't use the Black Materia herself? That's further evidence.
The trouble with that is, it never says that Jenova can't join, you just assumed it. Even if she couldn't by the time the reunion had occured (a reunion that I can't explain other than using the Jenova theory), there was enough Jenova in Sephiroth that if she couldn't neither could he IMO.
There's also no evidence that Jenova doesn't use the black materia herself, other than she used Sephiroth's body, which would require believing Sephiroth is in control to support it, which is circular logic.

Sephiroth's barely- formed foetus was directly infused with Jenova cells; he formed and grew with them in his body. That's a much closer and more powerful melding than the Clones have.
It is much more, but it doesn't justify Sephiroth having the power to control people across the globe, project images of anyone he wants (which are capable of transporting Jenova who despite all of the things done to her can still turn a small dismembered body part into a huge boss), transform and use illusionary attacks, and fly.
The clones, and even Cloud can't acheive anything along these lines, let alone approach the scale Sephiroth can use.
It's also quite odd that everything 'Sephiroth' does is exactly what Jenova would have wanted.

Jenova, on the other hand, was beaten by hte Cetra, sealed in rock for two millennia, dug up, dissected, stuffed in a tank, and ultimately beheaded. That's why she wasn't quite as powerful as she might once have been.
She flew through space and crashed into the planet with a huge amount of force and still took on an entire race. Her body parts can take on your entire party after being removed. I really think she could handle more than you give her credit for.

I won't go into the timing now, which also supports the theory, I think there's enough to go on.