"One thing I have tried to do is not go crazy with third party OS tweaks. I’ve tried to keep things simple by only modifying a few key areas that were bugging me about iOS."

If only more people would understand this. A lot of people think jailbreaking your device leads to performance issues and instability. It does not. It's the software that you install on your phone afterwards that leads to these.

I also enjoy tweaks that add features in a way that seems native to the OS. Some (random) examples:

CyDelete, Zephyr, Curiosa, Safari Download Manager, Bolt, Bars, F.lux, ShowCase, iFile, MultiIconMover, Reveal.