I want to put out a friendly reminder to make sure you test one thing before concluding that it is the OS causing the issues. There are certainly problems still with 10.11.3, especially with USB, but this one may be solvable. It was for me anyway.
I had problems from the time of the beta with wifi speeds on my MBA with wireless AC. Transfer speeds could take 25 seconds or more for an 8mb picture. It was terrible. After going through the forums I was certain the problem was Apple's and I didn't solve it until a couple months ago, right after 10.11.3 was released and didn't solve my speeds.
Realizing that my Asus RT-AC68U Router had done updates, I was recommended to reset the router to factory settings after the updates (which there had been quite a few because Asus regularly adds features/fixes). Guess what? After resetting to factory defaults and setting it back up for my network, my wifi problems were completely fixed. It wasn't the fault of the OS.
I noticed recently there was another update for the router. I proceeded and noticed over the next week that speeds sending to the server were slow again. I then reset the router, entered in all the settings again (which is a pain) and the MBA was back to full speeds on wifi. The router, like any computer, gets an update and things don't quite run the same or as well at times.
It may not solve everyone's problems, but it certainly did mine and I hope it does yours too, if you are willing to take five minutes and try it.