SE
No barometer (SE users reporting they aren't seeing elevation data in the health app)
No taptic engine
No 3D touch
Slow touch ID (first generation)
No 128 gb option
No LTE advanced
No 5 megapixel facetime camera
Also the SE screen is completely interchangeable with the 5S , so you are basically buying screen technology that was first introduced nearly 3 years ago.
There have also been multiple reports of loose power buttons. It's crazy apple haven't sorted this issue out yet, i had this problem all the way back with the iphone 5