This question comes up constantly: I’ve never been to Israel before and I only have a short time - often only a couple days - what should I see? So here is my suggestion.
I’m saying this from the viewpoint of someone who is most interested in Judaism and Jewish history. My personal mission as a tour guide is to acquaint Jews and non-Jews with exactly that - Judaism and Jewish history.
1) The Kotel (Western or Wailing Wall) - Given a chance to see only one thing, that’s it. For centuries, it has been the focal point of the Jewish people. Of course, the Temple Mount itself is the real focus, and Jews and Christians can visit there easily (setting aside theological/halachic disputes), I believe that’s something special you prepare for. The Kotel is a place you can visit just because you have time.
2) The Temple Institute - A group which is devoted to the reconstruction of the vessels of the Temple to use when the Temple will be rebuilt, according to Jewish (and some Christian) belief. They do a wonderful presentation of how the Temple operated.
2.5) The Broad Wall - The defensive wall built by King Hezekiah to keep out the Assyrians. It is right outside in public in the Old City’s Jewish Quarter (no entrance fee or anything), not far from the Temple Institute. It is the most documented event in biblical history - discussed in three different biblical books, AND immortalized by the Assyrians, from their point of view, on clay prisms!
3) The City of David Park - Next to the Old City it is the Old-Old City. The original Jerusalem, conquered by King David, started out outside the walls of what is now the Old City. They have the remains of what is believed to have been the palace of King David.
4) Israel Museum - Specifically, the Shrine of the Book about the Dead Sea Scrolls and the history of the biblical text, and the model of First Century Jerusalem. This museum has so much more, you should expect to spend a few hours.
5) Southern Wall Excavations (Davidson Center) - This is great to see if you’ve been to the Shiloach (Siloam) Pool in the City of David, because this is the other end of the process - the steps and gates where pilgrims entered the Temple Mount in the times of the Second Temple. The broken stones piled on the original Herodian road give a good view of what the destruction of the Temple meant.
6) Caesarea - How the other half lived, specifically the enemy. This site is so important to understanding the clash between Rome and Jerusalem that affects all subsequent history, and it is so well preserved. Rabbi Akiva died here and the Great Revolt started here. It even plays a role in the War of Independence.
7) Qasr al Yahud - This one may just be me, but I love guiding here. It is the traditional Christian Baptism site on the Jordan River, where John the Baptist is thought to have baptized Jesus, but from a Jewish point of view, it is none other than the crossing point of the Jewish people into the Land in the time of Joshua. Besides that, you are only a few feet from Jordan and often looking straight at Jordanian soldiers. At the moment, this is our least problematic border, so now is a good time to see it and maybe dunk in the Jordan while you’re at it.
There are obviously hundreds of other sites to see, but if you’ve got a short time, this is the order I’d start with. Most of them are in Jerusalem, because it is the center of our universe and where much of our history happened, besides being very accessible to tourists on a short stay.
Whether you’re here for a short stay, a long stay or have made aliyah, your own tour guide, like myself, can help tailor the experience to you and make sure you can really understand, “What am I looking at?”