I found this on Plane and Pilot. It has some good info on the FBO vs large academy question.
Prospective pilots faced with the choice of flight training schools have a number of ways to go. At the bottom of the training ladder (in price, if not necessarily in quality) are the Mom and Pop stores. These are usually tiny, local, one instructor-one airplane flight schools, and the tendency too often is to discount such simple operations as worthless.
The tendency is wrong. Don't knock 'em unless you've trained with 'em. What such schools may lack in a formalized training program, modern, state-of-the-art facilities and equipment, they may more than make up for in down-home aeronautical common sense.
At the opposite end of the spectrum are the large, well-organized, well-financed flight schools, often supported by a major airline and often with 30 or more airplanes available, ranging from simple, fixed-gear trainers to complex twins. Again, the naysayers sometimes complain that the larger schools are expensive, impersonal and so entrenched in a rigid curriculum that there's no room for individuality, either among instructors or students. As with the smaller schools, the truth probably lies somewhere between the best and the worst predictions.
One virtually unquestioned reality, however, is that the large, more structured flight schools have a definite advantage in turning out professional pilots in minimum time, if only because they have the equipment and personnel to pursue the goal continuously. No student need remain ground-bound for a lack of available instructors or airplanes when there may be a dozen instructors on staff and two dozen airplanes parked on the ramp.
Flight schools that specialize in airline preparation often offer benefits ranging from truly professional instructors who have seen it all to airline-oriented ground and flight instruction, and there's little question that this can be some of the best aviation training there is.