Not to come off as harsh, but the two are not even comparable. It's like asking, "would you rather get the flu? Or AIDS?". The apple device that compares to the One Plus 3 is the IPhone 6s. The SE is essentially an IPhone 5, a phone from 4 years ago. However, to answer your question the One Plus 3, I am not a big fan of the phone but in all ways, it beats out the SE.
Aside from what you said above, you have the SE on your list so if you are looking for premium phones on the cheaper side check out the Axon ZTE 7, has an unparalleled price to performance. It compares to phones 3 times it's price and is a serious contender, even with the newest flagships.