Hey Emunah,
Perhaps I can help.
I am an Israeli citizen (made aliyah when I was a kid). I went through the whole shtick...army etc..
I was rejected from Med-school here in Israel when I first applied. I had pretty good grades...both high school and standardized (Psychometry test).
Understand that Israel currently has around 400 seats for medical students in the "Israeli MD programs." Both Jews and Arabs see medicine as a noble and secure profession, and applicants are in the thousands. The bottleneck is so severe that more students are forced to study abroad than in Israel. The government doesn't wish to change the system because these students in Hungary/Italy/etc.. usually end up returning to Israel. This means that Israel gets doctors for FREE! It costs millions to educate doctors, and the fiscal interests of the country outweigh those of the students.
I was one of those students who was "forced" abroad. I chose the USA, mainly because I hold dual citizenship. I was extremely fortunate in that I did really well through college and was accepted to a US medical school.
The Israeli system also took notice and ironically I was accepted to medical school in Israel. However they made it clear that I would have to go through the whole process, excluding perhaps one year.
I was thrilled with the option to return home to my family. However my joy was shortcoming. You know what they say, "you get what you pay for." Since education in Israel costs next to nothing, there is no abundance of....umm anything. Now I don't mean to generalize, but there are only 4 schools here, so anything I say pretty much goes for the whole system, or at least a quarter of it
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American and Israeli schools are VERY different. There is almost no support system in Israel. You are on your own. Some may see the extreme independence as a blessing. I don't. I need a support system. I need a structure. I need someone to talk to (from the administration). I need tests...yup thats right. How can you go through med-school and not be tested

Here they expect you to breeze into class, study whenever..and take the test at the end of the semester (usually 100% of your grade). There is no strive for excellence at all. I was told numerous times by Prof's that I dont really need to come to class. Just pass 75 and you'll be fine. Well, I am sorry, but I am thinking of the patient here, and this approach does not sit well with me.
Here is my two agurot. If you plan on making Aliyah...truly...you should try to get in to an Israeli program. However they will not cut the corners for you. They don't give a damn if you are a zionist making Aliyah (they should). They will ask you to take the Psychometric test. Whle this test is easier than the MCAT, and can be taken in English, you will need to score very high. It can be done!!
If you decide to stay in the states, Aliyah will be out of the question for many more years unless you are well off financially. The loans....need I say more?
I am very unhappy in school now.....can't ya tell
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I let the US school that accepted me know that I am interested in accepting their offer afterall.
I hope that whatever decision you make you will be following your heart.
If you decide to stay in the US perhaps we'll be on the same flight to Israel in say...10-15 years. It will be your first and my second aliyah.
good luck