The stairs sequence: I somehow doubt that is going to be kept as is, I mean these days running up 30 odd flights of stairs is not anybodys idea of entertaining gameplay. So it might get turned into a cutscene, or have frequent fights or removed entirely. But if they did keep it in, they should change 'retard' to moron or idiot or something, because that could cause offence.
As for Tifa's desire to experience be rescued. Leave that in, shes a small town young girl at the time she says that, it's character development - and we see how when she grows up she can take care of herself, and doesn't remain a damsel (and even if she did I don't really think that would be a problem, there should be room for all character types and not just girls who can kick ass)
Same thing with Cid and Shera. You can't go changing plot points because they're uncomfortable. If you do that you might as well make Shinra a green energy company who never did anything bad to the planet
Clouds crossdressing. The situation is played for laughs - a macho soldier type man in a dress is funny - thats sort of the root of humor, a subversion of expectations. It's not the same as laughing at someone who is actually transexual. It's the difference between laughing at Caitlyn Jenner (to pick a recent example) and laughing at Terry Jones as Brian's Mother.
I think it speaks volumes that Cloud is still a much admired character - if anything Cloud gets lambasted for being emo more than he does for crossdressing - In fact I don't think I have ever seen anyone disparaging Cloud, or indeed any of the other characters involved, aside from Corneo and his lackeys.
Furthermore, it puts Cloud, and the player (this notional impressionable teenage boy that everyone is so concerned about) in the shoes of a woman being leered at by dangerous creepy men. I think theres something valuable in that. When Cloud throws off his dress and says:
"I ain't INTERESTED in a buncha scrubs like you!"
We all cheer him on, because those creeps are going to get what is coming to them. Anyone who reads that scene as those guys being somehow justified in their actions because Cloud mislead them....well people like that are already twisted beyond hope.