I've read through all of your thoughts -- thank you very much -- and I agree with user jlrwi that we're really talking about two kinds of commands here. One is the combined command, and the other is a SID / STAR / flight plan.
For now, just for the chained commands, based on reviewing a number of real-life clearances, I think altitude and speed should take effect immediately, and that there can be multiple directional commands that will be followed in sequence.
FlightID C ABCDE FGHIJ 3 S 180
... would mean cleared to ABCDE, descend to 3,000 feet, and reduce speed to 180 knots; then continue to FGHIJ upon reaching ABCDE.
The command parser would also support using multiple "C"s, like so:
FlightID C ABCDE C FGHIJ C 3 S 180
Then STARs, supporting speed and waypoint pairs, will have to be separate.
Unless there are significant objections, that's how I will do it.