Well, the first "assumption" that he can absorb the Mako isn't really an assumption. Sephiroth flat out says he gained the knowledge, it's there and it's an in-game fact.
He says he gained KNOWLEDGE, even if that's where he got it, he never mentions all the other ridiculous things he's meant to get out of it.

As for "uncharted psychic abilities"...two words: Manipulate Materia. If regular people can use this ability with materia, why can't Sephiroth do so after gaining the Cetra's knowledge in the Lifestream.
Sephiroth is regular, he's only crazier, and had a higher degree of modification than Cloud. Manipulate materia not only needs to be equipped, it isn't even on the scale as far as Sephiroth's powers go, he also demonstrates the ability to mutate for one.

Sephiroth, a "mere human"? Perhaps the whole point of what Sephiroth is slipped your mind. Sephiroth is someone born with the powers of Jenova who, later in life, went on to absorb the knowledge (and therefor Planetary power) of over two millenia of civilizations. And on a side note, Jenova is never seen to control anyone's mind or use any psychic powers.
Sephiroth was given Jenova cells, he did NOT have her powers, only a slight increase in strength and maybe reflexes etc. You are assuming everything about powers being absorbed. Jenova does all that mind trickery millenia before Sephiroth was even born.

Not really. It's never said anywhere that Jenova's wish was to become a God and rule over every soul. She just likes to devour life energy.
No but funny how Sephiroth's 'goal' involved killing the last Cetra, pretty much destroying the planet, and reuniting Jenova.

Not really. All hidden truths in FFVII are either revealed or hinted at in not-so-subtle ways before the game's end. Why should this supposed "truth" be any different? I'm sorry, but when it comes to a choice between your "sheer logic" and everything we're ever told throughout the game, from beginning to end, I know which one I'd pick to be correct.
You only assumed your first two sentences, and without anything to back them up. Anyway the game hints at it the whole time through, more through learning about Jenova and Sephiroth than anything else, then the last fight with Sephiroth can be interpretted in many ways.