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.
(To be clear, I'm not saying it's a matter of ownership and personal brand. But someone needs to start the project and form a team around it. I don't think they're worried about personal brand, it's more an issue of reverence for the franchise.)