It depends on what you are looking for. I live in Israel, and for obvious reasons have never been to Syria. If you're interested in holy places (of any religion, whether you're religious or not), in the vibrant modern state, in the incredible mix of people and cultures... then it's Israel. For a more "Middle Eastern" experience, Syria would no doubt fit the bill better.
Note that if you decide to go to both, you would have to go to Syria first, and not tell the Syrians you plan to visit Israel - they won't let you in if they know. Israel will let you in, after much questioning, if you've been to Syria.
Can't help on specifics of Syria, as stated above, but if you want a suggested itinerary for Israel you need to give more information. Your interests, will you have a car (public transport in Israel is generally excellent, but sparse in some parts of the country), etc. If I read your post correctly, you're looking to spend five days. I'd say at least three days for Jerusalem. You could easily spend three months or three years there and not see everything.