i'm not an airline pilot yet, but based on my experience of a consultancy that ran on meritocracy:
The company sold its self on meritocracy, but staff were given the good projects and treated according to who they went out drinking with. Essentially, if you were in with the in crowd it was good, but for those that weren't life was not all roses.
I can see that seniority at least gives those hard workers who might keep themselves to themselves a chance for the command course rather than being passed over by the "in crowd".