I unfortunately don't have much to offer that can actually be helpful. I (and I feel like this probably applies to many LWers) am not at all turned off by arrogance, and actually find it somewhat refreshing. But this reminds me of something that a friend of mine said after I got her to read HPMOR:

"after finishing chapter 5 of hpmor I have deduced that harry is a complete smarmy shit that I want to punch in the face. no kid is that disrespectful. also he reminds me of a young voldemort....please don't tell me he actually tries taking over the world/embezzling funds/whatever"

ETA: she goes on in another comment (On Facebook), after I told her to give it to chapter 10, like EY suggests, "yeah I'm at chapter 17 and still don't really like harry (he seems a bit too much of a projection of the author perhaps? or the fact that he siriusly thinks he's the greatest thing evarrr/is a timelord) but I'm still reading for some reason?"

Seems to be the same general sentiment, to me. Not specifically the SI, but of course tangentially related. For what it's worth, I disagree. Harry's awesome. ;-)