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Definitely not. A Half-Life protagonist has to be a blank slate that you can project yourself on, Alyx is the opposite of that.
I must have missed where she was mentioned to be the next protag tbh, I took it that Gordon was saved by the Vortigaunts and the mention of "this is my final epistle" was refering more to Laidlaw himself than to the character of Gordon Freeman. Alyx would be a bad choice as a HL protag. To be completely fair though, HL2 did not succeed in making the entire game feel coherent with Gordon as a mute protag and blank slate. HL1 did this better before and the absolute best game that perfected that design was Portal 1 (Portal 2 failed at that too, albeit still being a fantastic game).
For the silent protag to work you'd need to never have the player questioning why you are not replying to what is going on verbally. Only Portal 1 did this perfectly imo.