Given how limited Israel's military capabilities are, being based on defense, I don't know how they'd carry out an attack on Iran which is separated by at least two countries that would not be friendly to military encroachment, let alone Israeli military encroachment.
Israel's capabilities seem fine as far as I can see, not that I would object to their military capability being improved.
The usual scenario is that Israel will cross Saudi Arabia and stage their refueling planes over the Persian Gulf (but out of range of Iranian SAMs) and their fighter jets will strike directly into Iran from this staging area.
However, it is hard to see what Syria and Iraq could do about it if Israel decided to directly overfly those two countries. And it is hard to see Jordan choosing to fire on Israeli planes. I'm sure that there would be lots of whining if Israel overflew any of those countries, but whining is harmless enough.