Well, first, thanks so much for your work it's really one of the most useful tools on the internet imo. I'm not super qualified to critique it, specially the interface. (but I think it works well as is!)
I had a look back at it and see many great new features.
(1) I think it's awesome that you can program javascript inputs (and there's AVR8js). But it's not really user friendly: maybe there could be some editor window or something you could program js in with syntax highlighting
I think that's what would be most significant contribution for me, because there are quite a few prototypes where you want to mix analog/digital and that's currently difficult.
(2) If you want to get really fancy, look at editor.p5.js interface (although in terms of self-documentation[1], I think circuitjs is better!). The cloud save functionality could be really useful (although I'd understand if you find it out of scope).
(3) Maybe the time step could adjust automatically as an option? (Something like: auto step -- simulate at half speed and check the difference between the two simulations; if significant, improve accuracy until it reaches maximum; I'm sure there could be better approaches though like trying to find maximum resonance frequencies)
(4) An easy way to run it offline? I think since it's already a web app and it's very light, an electron app distribution would be nice (although HN notoriously cringes at electron :P ).
[1] I define self-documentation as the ability to find functionality and documentation within a user interface. That's easier done with GUIs where commands and references should be a few clicks away, though it can also be done in text interfaces with help commands and such.