I didn't experience the issue with the missions you are talking about either. I also went to Rivet City (and did quite a few missions there now) first, and haven't been to the GNR Station yet... nothing about skipped quests for me.
And the Kharma does something i can assure you. It changes the way people act towards you... there's at least one extra skill you can select when you level up that is also dependant on your kharma... some people will accept/refuse to be your "teammember" depending on your kharma level... etc. It DOES affect the game.
I've met quite a few enemies when wandering through the wastelands. Regarding the fact it's "wasteland" and there's supermutants, raiders, etc. It makes sense that there aren't many people out there who decided to have a comfy "dinner at the park on a blanket"? Or does it seem odd to you that they prefer to stay in the guarded cities/towns where they are safe and have everything they need?
I agree about the crappy animations, they look terrible sometimes. But it doesn't really bother me to be honest. I dunno why... but there are more important things in this game than great animations or fancy cutscenes (which i don't miss at all).
And about the weapons... i'll say it again... i think they've done a great job. You have your rock-it launcher, a weapon that can use almost anything as ammunition. You have the railgun which uses rail nails as ammunition... you got another gun that fires darts... a sword made of lawnmower blades which is in flames... mines made of lunch boxes and bottle caps (there's your use for bottle caps as far as weapons go).
Beside that, you have regular weapons... and it's not like there's not quite a few to choose from either.
Then you have futuristic weapons like laserguns and plasma rifles etc.
And on top of that, you get the special guns... like the Fatman, a gun that fires mini-nukes (like, come on! how cool is that?!).
I don't know... but tell me again... what exactly is missing? More weapons? A bow that can shoot bones... right.
Tell me about any other game with so much variation and selection regarding guns. I can't seem to think of one right now.
Maybe this game doesn't fit your taste, ever thought about that? Because it certainly is a very awesome game!