Season two of himawari is pretty much the same as season one in many ways, no surprises there. The difference, which resulted in a lowered score, is that there's too much "drama" or things they'd like to call drama. Instead of just the slice of life-esque episodic comedy thing we had in season 1, season 2 tries to be something it's not by introducing some kind of an enemy organisation that keeps on sending weird ninjas and doing experiments or whatever. As a result, there's much less focus put on the funny parts and much more on some kind of subpar "drama" or slightly serious stuff. This further enhances the flaws of a show that never had any remotely good plot in the first place by focusing on what it sucks at the most.
I have absolutely no idea about what they were trying to do with this anime, but it sure as hell wasn't well done. It's really a stupid move to stray away from the pure comedy thing they had going. It got really damn boring quickly and I have no idea how I even managed to watch it all.