Poor compensation: Yup, I'll cop to that. I could be making way more in "industry" but I make enough to live and I don't build ad-ware and do take pride in my work.
Being a PhD but little respect: I actually have the opposite experience. I'm not a PhD, I don't even have a Masters. But I can write decent software and I get respect and recognition from my PIs and other top-tier faculty that we've collaborated with. I feel like I've gotten just as much respect with my humble BS in Comp Sci from a state school than if I got a MS/PhD.
Micromanagement: I have the total opposite experience. I've worked with the same group for a long time, maybe that changes things. We apply for and receive grants to work on projects. We make high-level assertions for what we will do during the course of the grant and our PI gives us lots of lee-way to meet the goals of the grant in whatever technical way gets results, is FAIR, and open. Granted, I may have just lucked out here.