A few things here, so I'll take them one at a time.
Choices do matter, they always have. I've been explicit that even inconsequential choices might matter. I've mentioned this example before, but I'll hide it for those who want to avoid spoilers and walkthroughs.
The very first choice you make, whether to avoid Megan/Mom and go exploring, has a big impact, but not till much much later.
I think where you've read that "choices don't matter" is part of the FAQ, in the form of a question from the user. I had to tackle this as, in early releases, no-one was seeing how the choices were stacking-up, so they thought choices didn't matter.
I've also singled those that don't matter and there's only been a few: Choosing where you first went in the warehouse (you'll get lost anyway) and looking at Marie's pussy (she doesn't care). The rest have effects.
Yeah. Not getting all of the girls is a tough one, but only because it's being stacked-up against ALL of the harem games, especially on this forum.
The one thing I can say is that you won't be fooled into having something with somebody and then it's cruelly whipped away. I can't stop you thinking "I'd give my left nut, and one of the redheads, if she stuck around." but think of it like ships that pass in the night, or a one-night stand. People move on. Stuff happens.
Otherwise you'll be able to make choices and intervene to have the relationships that are available. BUT. Remember, that while you are the protagonist playing the game, all of the other characters are playing their own game.