I think Morsi would have been better for Israel. I believe that’s why the US tried to save him.
For Israel, having other religious/sectarian and right-wing governments in the neighborhood makes Israel’s government seem normal. Also, having a bunch of “bearded ones” to point at every time they want to convince the world that they are surrounded by… well, you know.
So far, El-Sisi seems closer to a Mubarak than to an Abdel Nasser. If he is smart, and really cares about what is good for Egypt, he wouldn’t run for president.