well first to get this out of point, no matter what you do - Israel will ALWAYS be targeted and one of the main focus of diplo games as there'll be 3 outcomes;
1)Israel gets artifically powered by having ~20 income per territory from scenario, making their lands very valuable and prone to gangbanging.
2)Nothing gets changed; the game starts and Israel, not making any big impact to game, either gets blobbed/puppeted by Egypt/Saudis or gangbanged because of RP, as realistically none of Israel's immediate neighbours love them.
3)Israel gets a city map to compensate, this keeps their lands in the same income but gives them artifically a lot of territories outside of the map, makes them lesser prone to gangbanging while still keeping them a main power without overridden bonuses.
Second, while you are right about giving *only* Israel a city map makes the map a lot of Israel-centric(which I can argue that Middle East *is* Israel-centric, even with ISIS stuff, but won't debate), you *DO NOT* have to only make one city; one problem of this map is that it has A LOT OF unused lands that could be otherwise put to use for things like this.
Let me demonstrate. I artifically moved the state/religion bonuses from Sudan area to Central Asia/Caucaus with my so-great paint skillz to open space and this is the result:
http://i.imgur.com/bhEiDBQ.png(...and yeah I know my orders can be seen in the map, don't care.)
See? That emptiness is about the size of Egypt plus Jordan, Palestine & Israel; that's roughly 100 territories. What's better is that Egypt & Jordan has a lot of large territories, if you make all territories the size of Israel ones you could get close to 200 territories.
Assuming roughly 40 territories is enough for each city(some can have more detail while some don't), this means you'll be able to put 2 cities at worst and 5 cities if you work for it, which is enough to include all major powers' capitals(Ankara,Cairo,Tel Aviv,Riyadh,Teheran) or some disputed/important cities(Nicosia,Jerusalem,Mecca,Istanbul etc.)
Now you may not like the idea of having city maps on the map or simply don't want to spend further time on this map as it's close to release, I can't blame you if you want to rush this; it's a tiresome job and it's your map after all, you are free to do whatever you want with it, I'm just offering suggestions to make this map even better and get the best quality out of it. So far, people seem to be interested in giving Israel realistic power without making it have 20 income per territory and the map has a lot of free space that could be put to better use, so this is the best way that can be gone I presume.
Anyway too much writing for one day, G'day.
EDIT: typos
Edited 6/23/2016 19:24:02