I do have a pretty solid complaint about back to the Future part 2, because if Marty goes into the future he should arrive in a future where he disappeared back in 1985.
They really should have introduced a new protagonist just for that section, otherwise it's not internally consistent with itself.
Hmm, i haven't played Alyx so I couldn't comment, but for trilogy i'd like to only stick to same protagonist in the same set of storyline, and since HL1 have different tone and set in different time and place and isn't flow so well into HL2, and Alyx feature a different protag, HL2 and the two episodic is just the perfect 3.