Ideas are cheap, but here goes :)

In my workflow I usually want to end up my work with applying a global effect on the whole timeline (like sharpen).

The easy route would be putting this into the rendering dialog. Something that would require substantial UI design would be having clip groups a first class citizen. Being able to apply effects and transitions to groups of clips just like you can on its children. But that would require to figure out how to "enter" the group and work on the clips inside.

Right now you can only paste an effect on all clips, but that leaves out transitions and makes it difficult to toggle an effect off to speed things up while working.

I vote for this feature. I'm pretty sure others have requested it as well. A slight enhancement of this is to allow effects to exist in their own mini-track, so they can start and end anywhere and apply to the composite of everything above them. Some other video editors allow capability close to this and it can be useful especially if you're trying to artistically apply a slow keyframed change over multiple clips. In one video, I wanted the hue to rotate 360 deg. across 24 short clips. Kdenlive would have required manual alining of keyframe values at 48 points (both ends of each clip), so I did this in another video editor.

A possible workaround for kdenlive would be to render the sequence to an intermediate format like dnxhd and re-imported the render as a single clip and applied a keyframed hue to that, but then your project is spread out into multiple EDL's and you lose the ability to tweak transitions and clip lengths without repeating the entire process each time you tweak.

I do realize implementing something like this is probably a pretty major architectural change.

We are evaluating the idea of having multiple timelines in one project. You could then use them inside each other as clips, which would make it possible to achieve what you have requested.
For now as a workaround you can do something similar as drosky proposed. Just skip rendering the "sub"-projects. It is possible to add kdenlive projects as clips inside another kdenlive project.

Actually, that's a pretty good work-around. I think I knew that you could load one kdenlive project into another, but I had forgotten that fact.