I wouldn't exactly defend Obama's Egypt policy, and I can understand politically why Republicans are taking potshots, which are nicely summed up in this Foreign Policy article. But most of the criticism is opportunistic. Not only can no US president control events in Egypt. It's nearly impossible even to influence them. What's going to happen is going to happen.
This is a natural phase in the Arab Spring. Yes, I still use that term, because I take the long view that what started in Tunisia and Egypt two years ago was the beginning of a process that's going to take probably two generations, or 30 years, maybe more.
It was inevitable that the first round of elections in a newly democratic country was going to be won by the most nationalist-right party. There are many reasons for this, among them the fact that the liberal groups are ill-financed and fractured, but mainly just that the nationalist-right party offers the kind of xenophobic appeal that most people will fall for before democratic habits of mind are established in the larger people, which takes a long, long time.
Democratic habits of mind...this is the key, and it doesn't come easily for any society. Took the United States a good 100 years. With regard to the treatment of black citizens, 170 years. These habits don't exist yet in the Arab world by and large, except to some extent in Lebanon, which unfortunately is functionally run by Hezbollah, and a few other places.
Now I think they can get there faster than the US did, because of technology and information and so forth. But it seems to me a reasonable expectation that the current generation of leadership is going to resist dramatic change. The next generation, the people who are now in their 30s, will be the first generation to be willing to liberalize their societies in ways that will make a difference, and that should happen in about the mid-2020s. But they will go only as far as the populace will permit, which probably won't be that far.
Then, another 15 or years after that, I would expect some real change to happen. By then, Wahhabism may have abated. Technology will hopefully have made economic glasnost inevitable. Some scholars and intellectuals will have reconciled Islam to secular government in ways that majority opinion can accept. People will see that you can have free speech without it bringing down society. And, of course, education must spread. Years of educational attaintment are pretty dismal across the region, as are teachers' salaries and other indicators of the value placed on education (starting salary for teachers in Egypt: around $20 a month).
Anyway. There is not a whole lot the United States can do about this process. It will just have to play out. In fact, on balance, we should probably stay out of it for the most part, except when we can do something quick as we did in Libya, preventing a planned slaughter. I suppose we could, at an opportune moment, do a Marshall Plan kind of thing, but the $14 billion the Marshall Plan devoted to Europe is $100 billon or more in today's dollars, and of course the people now yipping at Obama for a slightly ill-considered comment by his ambassador are never, ever going to permit anything like that. So we will be largely bystanders, which isn't great, but it's better than starting wars, assuming we have the sense to stop doing that.