It's mostly because circuitous jurisdictional turf battles. The bacterial approach involves applying something to the mosquitos to kill them, rather than modifying the mosquitos, so it apparently counts as a pesticide, which puts it under EPA purview. Producing genetically modified animals is subject to FDA review instead. Apparently the EPA has a lighter touch, as the Wolbachia mosquitoes got approved by the EPA for use in the same area that was originally going to be the site of an Oxitec test in the Keys that got squashed by the FDA.
See https://phys.org/news/2017-04-florida-bacteria-infected-mosq...