It depends on what the Flight MA represent. In the full MTS, you have to choose Ground Effect, Hydrojets, Thrusters or Gravitics, each of which has their own quirks and limitations. The obvious one for thrusters is they require fuel, but that assumes your setting tracks that or cares. It's basically fluff considerations.
I will caution you not to expect the MTS to give you combat-balanced or cost-effective designs; it doesn't. It's intended to give you gameable stats for the props in a roleplaying game, not act as a unit constructor for a wargame.