I like the idea very much - as the beagle-family is a great target for this kind of course - i think!
did you just try what the pocketbeagle-2 does out of the box?
(for me there are in the mail now ;-))
the first and most important questions for such an idea are:
- what is your target audience
- what are your learning-goals
- what is the background information your audience brings with them
if the idea is to do something more classical / theoretically maybe something in this direction:
- in the stock linux system
- very high-level python / node-js / bash - play-around with some leds and an button / webpage
- how to automatically start such an application on system-startup
- play with LED-PWM / I2C or SPI sensors / Pixel-LEDs / RS485 / DMX or similar more hardware related things
- maybe use the RPU for some fast counting actions? (as fare as i have read that is in no way trivial to understand/learn)
- maybe have a look at Status Zephyr support for PocketBeagle 2?
that would go into the direction bare-metal (without an real OS)
personally i like it more to do real projects that have a HW part to have something real / moving on the table…
all with there own sort of problems you could run into and therefore learn the best ways how to design a system / where the edge cases and so on are..
- classic light-barrier / watch-stop (something relative fast crosses two light barriers - the program has to stop the time from the first to the second and try to calculate the speed..
- could invole into an (very basic) coin detection thing (more light barriers.. doing very accurate / reproducibly time/order patterns…
- small balancing robot (PID / similar)
- there are so much more ideas…
and they are not new. the art here is to do the course-design in a way that really makes you want to participate in / have fun doing it..
maybe this is some kind of inspiration - maybe i have misunderstood your request completly 
sunny greetings
stefan