Firstly, Jerusalem holds importance for Islam and Christianity along with Judaism, so Israel cannot possibly restrict one. But they still do restrict Palestinian Muslims, while allowing non-Palestinian Muslims access; ethnic discrimination.
Secondly, Mecca or Medina are not illegally annexed cities under international law, are they? Those cities have been under Muslim control since the 6th century continuously. It wouldn’t be a problem if a city with only Jewish control and presence didn’t let non-Jews (religiously speaking) in, but Jerusalem has been fought over for AGES and like I said, holds importance to the three Abrahamic religions.
Thirdly, even if what Saudi Arabian government does is wrong (oh hello, another one of strongest US allies), does that validate the behaviour of other states?
As for Western Sahara, you are absolutely right about the illegal occupation.