highly doubt an academy is the only option. And the only reason i believe most people are against academies is they tend to sugar coat things a little much and show a great emphasis on the potentially positivie instead of the potentially negative aspects of a flying career, and in many cases have been known to make empty promises to potential students and alumni alike. The other major complaint about pilot factories is they cost an extensive amount of money, which tends to place the pilot who finally completes the academy severly in debt which may be difficult to recover within his/her lifetime.
Same token, any good university can place a person severly in debt. The difference as people normally state is you could get a degree in something that'll allow you to pay it off, however, the vast majority of people i know are struggling to pay off their university debt, and will be struggling to do so for years to come.
To mike, no...what you describe is a FBO, not a factory of any kind.
Another thought on the academy's though, it would seem like the airlines would really like the academies especially if they were able to provide them with the curriculum they'd like to see. It would guarentee standardization from the pilot applicants experience level, and as a result, they would have people that would be geared to pass initial training. Which, would probably improve pass ratings and level the playing field for the airline.