I agree with most of your points. And I totally understand your frustration.
1. The tools are getting in the way - that was one of the reasons I left Axure after years of working with this tool. The interface is too heavy. I expect from a design tool (at this level of granularity) to be context aware and well designed.
Designing tools for designers/tech people is particularly hard. I can't imagine more demanding audience. You should see our user testing sessions ;).
We've spent months trying to figure out design that will fit experienced designers and newbies. Currently in UXPin you can hide all the panels and operate on a clean canvas using search +add function.
2. Too much control
It all depends on the project you have on your schedule. The level of fidelity depends on people you're working with, deadline, type of user testing you're planning etc.
3. Responsive design
I absolutely agree. We need to have tools for designing responsive layouts. Keep an eye on our new release next week.
4. Version control
Absolutely. We've got it. I can't live without it.
5. Export
Personally I don't find it necessery. Having link to a html version is enough for me. Our customers though wanted to export PDF and JPG, so you'll find that in UXPin.
I don't mean to brag, but perhaps there is a tool that fits your needs :)