I've made some of these suggestions before but time has passed so I'll mention them again here.
Level-based logic. I can't think how logic gates could be made to work in a signal milieu where edges — trigger pulses / transitions rather than logic levels — are the carriers of information. To me it looks like a nightmare of propagation delay conflicts, race conditions, and the like. Given the extraordinary creations of hoiktronics masters the limitation here could well be one of my engineering imagination, not of the system itself.
Still, if level-based wiring were to be introduced, along with at least NAND gates (from which all other gates can be constructed) but ideally a variety of pre-built gates, I'd be quite pleased. Naturally this couldn't replace the existing system. It would have to be an additional layer along with it. Feasible? I've no idea, haven't read the source code.
Programmable timers. Something you could tell to emit a pulse at a given
clock time instead of after a certain interval. I'm thinking dusk-to-dawn streetlamps, automatic Daybloom/Moonglow harvesters, and the like.
Obstruction sensors. Pretty straightforward. If visible pixels are in the block being sensed, the sensor produces one output state; otherwise you get the other state.
Oscilloscopes. For repairing plumbing, of course!
[eta] Oh, yes:
NPC attractors. When actuated these would attract one or more specified NPCs. You could make everyone head to your bar/restaurant in the evening, for instance, or up to the rooftop garden at sunrise.