I don't know what does or doesn't cause this. I think it all depends on how you use your iPad. I'll tell you a bit about my experience.
Personally, I bought the iPad back when it first came out, it was a beast at the moment. I used it as my main computer for a while because my white MacBook had a broken screen. I loved using it every single day for the majority of the tasks that I usually do. Then I got a MacBook Air, so the iPad was put to a side for a while. I use it for the occasional movie on a flight, a few video games and simple sketch drawings. Nothing too sophisticated.
I noticed that with the passing time, it got slower and slower. When iOS 9 came out, I did some research, and most people said that it made the iPad more responsive. Sadly, it wasn't my case. I wasn't alone in that ship either. I read reports on these forums of many people regretting updating their 3rd gen iPad to iOS 9. But it was too late for me. So I put it away in a drawer for months. When I turned it back on, it was even slower. Figured I should do a spring cleaning. I deleted most of the apps. Turned off all unnecessary options (motion, multitasking gestures, etc.). Still nothing.
Just last night I decided to reset it and set it up as a new iPad, not from a back-up, and installed just a few apps that I constantly use. Now it is kinda usable, but it's still lagging on simple tasks like downloading an iBook file or making a Skype call. I honestly feel that the whole experience has become way too sluggish due to the update. It's like it's telling me, "please get a new iPad". And I'm among those people who actually believe that Apple limits the processor/graphics/chip with each software update, making it less and less usable, until a person feels, "oh, this is too old, I'll buy a new one". I hate that