From interviews with the Alyx devs, it really sounded like the only reason they didn't call it HL3 was fear of not living up to the name.
Given the org structure at Valve, it's going to take someone with massive hubris to say "I can be the one to lead the HL3 project."
That or Gabe getting off his megayacht to lead it (or tell someone their project is worthy of being called HL3).
pretty sure they don't have a totally flat org structure anymore but I might be wrong
They decided to make it a prequel for fear of not living up to the name, the decision was made much earlier. If you're at all familiar with the contents of Alyx and the Half-Life franchise it wouldn't have made any sense to call it HL3.