Training
Everyone has a style and approach to training that suits them best. The FBO offers a closer home town feel, but often lacks in true expertise, equipment and availability. The ATP style has a fast and action packed "get er done" way but has higher costs due to newer equipment and higher overhead at the larger metropolitan airports.
The best answer is to not go to either and buy yourself a Cessna 152 or piper tomahawk and hire your own freelance CFI.
Skyhigh