Given the reports of Abrams getting frustrated over CBS not stopping TOS merchandise like he demanded, there could be some truth to the whole big ego/smug/hard to work with angle to it. It's the first I have ever heard of this, and I usually hear nothing but nice things from everyone to the point he's mentioned by his first name "Oh J.J. is such a great guy, J.J. is a visionary, J.J. walked my dog". I think many tend to forget that for a long time before he gained such a huge fan-base over ALIAS and LOST that Abrams had largely been known as "Jeffrey Abrams", just another Hollywood hack writer and executive that helped churn out some of the most generic product of the 90s that included "Regarding Henry, "Gone Fishin'" and "Armageddon".
Of all his work, I think I only genuinely liked the pilot of LOST, the only episode he directed for that show. In fact, that was the only work I've seen of his when it was announced that he was gonna work on STAR TREK, so I had some high hopes, especially after the Berman & Braga years. Then I saw his other work... Can't say I was impressed.