I use the pen almost all the time. I carry the phone in an iBlazon holster on my belt, so it's almost no problem. (I have to fight past it to get to the pocket in some jeans.)
I removed the bloatware by installing Safestrap and a few debloated ROMs. (The stock slot is still the stock ROM, so it's fast and easy to return to stock.)
Love the phone. But if you want one-handed operation, it's a bit large.