There are a few problems.
Some people do use Flygon as a secondary stage 2 line because of Rainbow Float. But it's just that, as a tech, even, free retreat isn't THAT great in practice compared to other Stage 2 techs, like Maternal Comfort or Dark Palm. Whereas these tech cards carry unique abilities, Flygon's free retreat is only neccessary in a deck that focuses on abusing such a thing. Secondly, it's poke-body can be achieved using a simple switch, and 3 Switches versus a 1-1-1 Flygon line or 2 Switches versus a 1-0-1 Flygon line generally has about the same probability.
The additional catch is that you need to have the same energy on Flygon as whatever you're switching with it. In decks focused more on acceleration, this becomes somewhat of a hassle if you want to retreat, as you need to place energy on Flygon and the active pokemon. Otherwise, you need a means to control energy.