I like the user interface and overall design. Also very nice onboarding of just logging in and trying the app.

Based on the title I thought that the pop-ups were the USP, but reading your post I am glad that you see it as just another feature because tbh I think it's kind of niche. I see the thinking, but in practice I think there's a few usability issues

It's kind of jarring to just move your mouse across the screen and accidentally hit a shape with pop-up and have the whole screen just blast a different color. And I only set it it for one shape, if I had multiple, I could easily see it getting very annoying. OTOH, I am not sure how you fit in buttons into a diagram when you're trying to keep it clean.

Speaking of jarring, probably a good idea to dim (or overlay to hue-shift, or filter like blur or texturize) instead of changing colors across the whole screen.

Honestly, I think I might need to see some better examples to be convinced because I would rather just click next slide for presentations I definitely don't think I'd hover over different elements through a mouse. And I'd probably prefer a labeled slideshow for user guides. Something that's low-tech, easy to embed, easy to understand. If I put time and effort into well designed popups, I don't want it to be suble and out of the way because then people might miss it.

I think I would much rather have different states for scenes, and have the option of switching to a state by hovering on a list of menu options (maybe organized into sections with a collapsable ui element). That would probably be pretty useful, and from there it's pretty trivial to add event triggers on shapes to active those state transitions instead. If through A/B testing, people like it then, great. If not, the ui controls are a pretty solid feature.

Also as a side note, I drew an ellipse and adjusting the upper left hand corner triggered what I first thought was a bug that caused the ellipse to become flattened (height of 0). I think what happened is that it snapped to something on screen in a way that wasn't obvious. I get that there's lines to show snapping, but it aligns with too many things (e.g. I had a polyline with a few nodes), and it's really bad if it's zoomed out where a normally large sized shape (400px) dissapears by moving the mouse a few pixels because it's zoomed out (so now it's 30px) and the snapping threshold is almost the size of the object, plus it's now aligning with things that were previously off screen.

Anyways, Good luck!