You only assumed that, and if he just happened to gain the same powers Jenova already had it's a pretty huge coincidence.
Right... he's got Jenova's essence within him already, and then when he becomes stronger, he gains more of her powers - that's a 'coincidence'? Seems natural to me.
So he can get to near God status through going for a swim in it, but he decides he wants to destroy the planet just for that extra push?
He was beginning to bond with the world ("I am becoming one with the Planet..."), and that's where those powers began to emerge. Summoning Meteor wouldn't destroy the Planet per se, rather it'd unleach a huge amount of Spirit Energy (from all the lives lost, and from the energy needed to heal the wound) and that's when he'd amass the remaining energy.
Hojo knowing that would suggest he knew Jenova could survive while split up. There is no evidence Jenova is incapacitated. It's weakened, but only compared to it's former self, but it's still damn strong.
So Jenova allowed herself to get sealed in solid rock for millennia, then let Shinra scientists cut her up for experiments, then let Sephiroth cut off her freakin' head, then just sat around in a tank for five further years, all of her own free will? 'Cause she was bored of world domination or something?
The reunion would restore it fully though, and is far more beneficial to Jenova than Sephiroth, as I can't imagine Jenova letting a human rule anything once she was back to full strength.
Sephiroth is the closest thing she has to family; a 'compatible' being who shares her goals and superiority complex, for whatever reason. She can't personally bond with the Planet; she needs Sephiroth for that, but she can join with him - as we see in Bizarro Sephiroth. Besides, if Sephiroth became 'god', he'd be far superior to Jenova.
Even after going through his time in the lifestream Cloud could still kick his ass.
Still, it took quite a few goes - Bizarro Sephiroth, the burgeoning God, put up quite a fight; Safer Sephiroth even moreso. It was only then, when his power had been worn down, when he was reduced to his Human form - Cloud was finally able to beat him, by unleashing five years of pent-up anger and hatred. 'Sides, that's how it always goes in the Final Fantasies - the 'final boss' has to be capable of losing to the heroes (who spend their entire quest gaining strength and magic, by the way) or else the plot wouldn't really mean anything. Would you play a game with an unbeatable final opponent?

Sephiroth is by no means ridiculously strong, Jenova treatments of SOLDIERS just wasn't very well developed in his day, and he was strongest.
He was the best, a veritable legend in his time. He was always distinct from other Humans, right from when he was a child. He was more than just another Jenova-injected SOLDIER member.
His will wasn't strong, he let Cloud beat him in the reactor. Cloud at the time was at a severe disadvantage.
Well, Cloud had got a lucky shot in and attacked Sephiroth from behind while he was standing, gazing into Jenova's storage case. Sephiroth was wounded, so Cloud was able to overpower him and throw him into the Lifestream. Cloud had one 'power' that Sephiroth lacked - the righteous anger brought on by the destruction of Nibelheim. Sephiroth was oblivious to the concepts of home, family and love; he had no idea of the strength that they provide. Consequently, he completely underestimated Cloud's potential at that time.

You can't judge a character's strength and abilities solely from the games battel mechanics, like HP and MP. After all, it's easy to make Yuffie into the game's strongest character, with greater speed, strength and magical ability than anyone else, including Safer Sephiroth. This doesn't mean she's a higher form of life than him or anything.