Ah I see. Well that hasn't been an issue for users for ages. Only a few important libraries are installed in the small root partition. Everyone will see it as 80/90% full, it's not a problem. All the programs you install from Cydia are now installed on the main partition. It makes NO difference how big the root partition is. That's only important for developers. And no you can't change the partition size, it's set at the iOS image creation. You'd need to create a custom firmware. But like I said, it's not important.
That's odd. Your options are to remove some programs or google how to mess around with the root partition. I wouldn't recommend it, its quite complicated and you can mess up the phone leading to a restore.
As of yesterday, after the time that you posted this, CoolStar updated the Stashing for 10.2.
It was recommended against using YUCCA utilities for stashing, because it went overboard. Saurik called the dev out on Reddit, which is something that he rarely does. The dev Coolstar (aka Clay Freeman) is a long time contributor and Saurik (Jay Freeman) says that Stashing by Coolstar is OK. ( It seems that the two Freemans have no relation)