Merge commits suck.
My biggest issue with GitHub is that it always squashes and merges.
You are aware you’re talking about two different pieces of software?
Yeah, I am. However GitHub, being the biggest Git hosting provider and all that, makes you use merge commits. FF-merges must be done manually from the command line. While this definitely isn’t a problem for me, many people out there just don’t care and merge without a second thought (which, as I said in my comment, results in having to create a new branch and cherry picking the commits onto there).