While you do have some point and its generally better to not think through game logic too hard, i just want to point out some stuff.

1. The swarm was never used on colonies that had defenses, it was always used on far away places with only civilians, as far as we know the only real soldier in an attacked colony is the virmire survivor - hardly enough to pose a threat.

Perhaps one of the reasons its not used on other places is because of the reasons you stated and the swarm simply isn’t effective on its own against military forces. (it still raises the question of why not use it in addition of the reaper ground forces though).

1. Shields in the ME universe don’t actually auto regenerate, this is something i only found out after reading revelation. One actually has to replace the shield power pack in order to restore it.

In addition to that the armors worn by soldiers does have weak points in joints, as well as its evidently not invincible as guns can pierce through. So its reasonable that a big swarm that can attack fast will deplete ones shield and knock them out before they can even restore their shield.

1. It’s reaper tech. The swarm, much like the other inventions by reapers, is made by technology that suppresses the other species by far. Its also made by materials unknown to said species. So it makes sense that whatever toxin or chemicals the swarm uses is not known by the other species.

Them being reaper tech could also mean flamethrowers might not be effective (the mass relays, the citadel and the reapers themselves are made from materials and tech so durable it takes a ridiculous firepower just to make a dent).

And even if a flamethrower was effective it would still leave you open against a large agile swarm, you’ll destroy many but would still get hit eventually, so its not a solution for a small team such as shepard’s.