I have mostly 4s and 5s on my APs but I have two 3s on two AP tests. I have nothing lower than a 3. So I’m wondering if this will lead to a higher chance of rejection?
You should be fine – two 3’s will not be the reason for rejection. I got in with two 2’s.
Don’t be worried. Passing APs is definitely a good sign that you understand the difficult material well, especially if most of them are 4’s and 5’s. I got in with 5 3’s, 4 4’s, and only 2 5’s. Although, tbh, my AP scores generally improved over the three years.
Honestly I don’t think AP’s are that important in general… After all you can choose not to send as many scores as you’d like. The primary purpose of AP’s is to get college credit for or skip courses for which you get a 4/5 on the AP exam.
Of course there are certain national awards you can win with a certain number of 5s, but since you’re applying to MIT, you probably already have other awards that are of much higher caliber. Even if you don’t, those AP scholar awards are so common that I doubt they matter much unless you get the highest one. Esp. when applying to an institution like MIT.
As far as I know admissions tests (SAT, ACT) are far more important than AP scores.