Now to the OP, I agree with most things you said. I wouldn't get rid of the gun or replace it with a tomahawk because sometimes there are those players who insist on being on the roof. While throwing knives are often effective against these players, they aren't always, and sometimes there is nothing more satisfying than shooting that roofer in the back and punishing them for ruining the match(you know how it is: all a game needs is one roofer to send everyone to the roof).
I don't mind them taking out Boost Cooldowns, but I think it is more of an issue of some perks or abilities being clearly more useful than others, like smoke bomb. What Ubisoft should do is make more(quantity) versatile abilities like smoke bomb. These abilities and perks should be much more pick and choose, and should all be much less obvious choices.
But, Ubisoft has been working on this game for almost, if not already, three years. The multiplayer component is probably past the point of "taking suggestions" by now. I also hope to see a beta that is not exclusively PS3, but we can't have everything go our way.
Besides, it's not like it made a difference...