Well, out of curiosity, then what happens when a proposed structure exceeds height limits, exceeds setback requirements, and doesn't satisfy the minimum parking capacity called for by the proposed site's zoning?
You (the developer) then apply for a PUD and then attempt to work with the city on a solution that works best for all parties. As an urbanist and graduate architect, I have no problem with the scale, setbacks or architectural design for this project. If it were me, I'd probably do something different, but to each his own, as long as it enhances the urban environment and pedestrian scale streetscape. At this point, I believe it does that.
I think the real issue for debate is parking. However, my focus would be moreso on speeding up fixed mass transit solutions instead of increasing surface or structured parking. I'd be open to developers of infill projects like this paying into some sort of transit fund, in turn of reducing their parking requirements.
I'm cut from a different cloth, so I'm much more accommodating of higher densities and less accepting of sprawl than the average Jacksonvillian. Yet, I do understand nearby resident's concerns and believe that the development group should work with the community on a compromise that works for all.