I haven't been on these forums in a long time (almost a year? Wow... Hi there strangers) but I'm so glad I did today and chanced upon this thread. This is just the sort of project I'd like to get my teeth into. Of course, this is your baby and I don't want to feel like I'm taking that away from you, but I've downloaded your GitHub code and Qt5 so I can look at them and understand what you've done. I'll say though that I'm mostly excited by the tool/plug-in possibilities since I'm a mathematician.
A few notes on things I though of while reading this thread so far:
UI
Personally, I think the main goal should be getting the most workspace efficiency, i.e. maximising the viewport/toolbar ratio. Basically, Hammer's UI is fine, just a bit old really. I'd say no to floating, GIMP-like toolbars and yes to something tab-based that can be hidden at will. Having plans for plug-in tools means their interface needs to be considered too. Since there could be quite a few available at once, something like Blender's spacebar search would be sensible in my opinion.
Tools and Plug-ins
Clearly a great idea and a much needed feature. I have no idea how one goes about implementing a plug-in system so I don't know whether you'd have to at least keep it in mind now or if you could just add it later. As for the language, I personally like python, but Blender python sucks and lua seems more suitable. Not my field, just my thoughts on that, for what they're worth.
My last note would be that everyone seems to be discussing the design, mainly the UI, as though it needs to be done right first time or else it will fail, but I'm sure you know that's not true. I don't think anyone actually believes things need to be done right straight away, but it seems everyone is being stuck up on getting the idea right before any code is written.