I'm not going to mention anything where it's just a matter of your taste in games being different than mine--anyway, I didn't really experience the problems that you did.

If you're one of the people who accidentally killed Goatmom your first playthrough (or any, I suppose), the tone is a little jarring going from that to meeting Sans and Papyrus.

I think Flowey's monologue after you exit the ruins is meant to make you go back and try to spare her.

Even if it's only at the end of a True Pacifist run, a run button for Frisk would be appreciated.

I get what you're saying, but it would break the rhythm completely. It's a "feel" thing. What we really needed were a few better fast-travel options to use during the True Pacifist ending.

Genocide has no difficulty curve, just a flat line with two increasingly massive spikes.

At the same time, it's not really meant to be fun. Dreary music, grinding for random encounters, etc. The game tries everything to get you to stop. Making it boring, putting up huge difficulty walls, emotional means (Papyrus) etc.

All that stuff about Chara

This is your criticism that I have the biggest problem with. People start the game hating Flowey's guts, thinking that he's the source of every problem in the Underground, wanting to kill him. And then when they get to the true pacifist ending, they realize they had it wrong.

And then, eventually, they start hating Chara and believing they're the source of every problem in this world. It's just shifting the same attitude--an attitude that you just realized is deeply flawed--onto another target.

Everyone wants an ending where you can save Asriel. But the greatest achievement you could have in this game, thematically speaking, is to spare and forgive Chara.