If you want to stay on iOS 9.3 take care that you do not accidentally update because you won't be able to get back down. While there hasn't been a jailbreak since iOS 9.1, having a lower firmware version installed could increase your chances of being able to jailbreak in the future.
They would Only need to start from 0 if Apple have closed what holes the jailbreakers have found in 9.3 in 9.3.1, which would be unlikely as there hasn't been a public release of a jailbreak for 9.3, I'm sure there will be a jailbreak out soon for an iOS version that's still being signed
hm, I lost my hope for jailbreak. Apple also lost my money for iphone. I stuck on 9.0.1 and until this 6 plus gets outdated I'm not buying anymore this product. Not that android is wonderful but I might look into it. Sad story that jailbreaking is almost dead, no more a bunch of groups working on it, people lost interest apparently. It was nice since iphone 1 but now iphone is just a closed system like those toy phones for kids. No thanks anymore.
What do you mean anymore? This is a rinse and repeat process: new iOS version released, new jailbreak made after some time has gone by, previous versions not signed anymore.