@Matthew Greco I think it would really depend on the merits of the deal in question as well as your long term goals. If you can find a deal that cash flows with only 3.5% down, then I would say go for it. The less cash you have to tie up in order to secure a deal, the better. However, it would have to be a pretty phenomenal deal to cash flow with that little equity but if you find one, good on you. Also keep in mind that with FHA loans, you will have to owner-occupy. If you're house-hacking and want to use the FHA loan for another property later on, you will have to refinance the first property (most likely into a conventional loan).
To address the OP's original question, the benefits with going with a 20% conventional loan versus a 3.5% FHA loan would be (1) not having to pay PMI (2) having an advantage when making offers on deals since sellers typically prefer conventional loan offers as opposes to FHA. But again, it would really depend on the merits of the deal in question.