Mine's got a lot more comfy, I guess it was the switch from a hybrid that got to me. Still yet to put my flat pedals on as I'm missing the right spanner! Most annoying things currently are the horrible rubbing noise I get when I use the brakes and the uselessness of the gears - it's constantly clattering and pinging when I try to change down in particular.
The brakes you'll get use to and should settle down after bedding in. Best to double check, my rear pads wore at an angle it meant i had to bin them before the end of their useful life. I'm getting the same with gears, Im fine -tuning now it till i get the right feel- to be expected after initial cable stretch. Big headache for me is not sure if I have a stiff chain link or badly align front derailleur, every now and them the chain jams against something and i have to pedal back then forward to release.