Mostly the "omnipotent Aerith" idea. She has some ability to influence the lifestream but I don't think she has anything resembling "control". Sephiroth can beat her in a 1v1 and has better control over those "extra powers", the major difference is Seph is going AGAINST the lifestream, and Aerith occasionally can get the lifestream to go the same way as her. The lifestream is super powerful but it's shown multiple times to not necessarily follow what Aerith says. She will likely obtain more control over this for part 3 but I don't think she's going to approach even majority ability to control things.
Though I also disagree with "Aerith in final scene is Jenova". I'm not saying he's wrong, he could be right, but I don't think I can 100% say it is Jenova. That said, I do suspect Cloud will continue to see Aerith between the start of part 3 and him handing off the black materia and THAT will be Jenova, just I think the final cutscene is force ghost Aerith, heavily because of Red XIII sensing her.