Interesting question.
with more forces to use against Syria, you might very well see a 5-4 day war instead of 6. the assault into Syria only started in the last couple of days. this way it can start on day 3, as soon as the main Egyptian line collapses.
The issue of Jerusalem will still be a problem. Jordan isnt just going to give Jews access to the temple mount, and any peace deal will still only happen in the relative far future (decades). what role will Jordan play all this time? it didnt intervene in the 1973 war, so if they do the same in 1967 how does that change their policy? they will get alot of flak for this from the arab world.
Of course, without the capture of Jerusalem and the WB the settlement movment as we know it will not exist. you still get small settlement in the Sinai, however they will likely wont be very large and will be removed as soon as a peace deal can be reached following an alternate 1973 war (assuming there is one, there probably will be however. maybe not in 1973, but during the 70's Egypt will get new toys from the USSR and will eventually be able to fight Israel on a slightly more even footing. also as soon as Sadat comes to power or a similar person, you at least have the chance of a peace deal with him. it was the grand victory of 1967 that convinced the Israeli leadership they were invincible and thus had little reason to negotiate.).
There is also the issue of water of course, and the fact that without a peace deal Israel will still be nervous about Jordan (since it can easily strike and cut Israel in 2 in any future war). without the OTL natural border of the Jordan river and the strategic locations around it, the IDF will develop differently in order to counter a possible Jordanian assault (as unlikely as it is).