Making treads slower as a whole (and removing the extra slow-down with additional treads) is one way of doing things. But if this is combined with nerfs to HCP storage units, it could get ugly for the combat-minded player.
I wonder if you could simply increase the penalty rating for treads a decent amount and remove the slow-down with additional treads. That way, if you use just two propulsion slots and stack a lot of heavy gear, you WILL be slower than before (250-300 perhaps?). However, you could counter-act this by using more propulsion slots to keep under the support limit (170-200 speed perhaps?). Do the same with legs and let them be about 100 speed while under the support limit and ~250 while well over it.
Then there would be roughly three distinct options:
1. Use two slots for treads, stack as much power as possible, and be very slow (250-300 speed).
2. Use multiple slots for treads, keep under the support limit, and be slow (~175 speed).
3. Use multiple slots for legs, keep under the support limit by avoiding some of the heaviest but strongest gear, and be medium speed (~100 speed).
Using two legs and going overweight should be a poor option. As should using wheels, although currently I don't think there is ever ANY situation where I'd equip wheels, they're that bad.
Then for hover units you use multiple slots for 30-50 speed with more specialised gear and lesser firepower. By the way, currently hover units are a much greater strain on energy and heat than flight units, because of their slow movement compared to flight.
Regarding flight units, you can move Imp. Flight Unit to rating ~*7 or so and appear only at the endgame. They can retain their low support value as their only downside, and maybe the integrity as well. For other early flight units, heat can be increased rather safely to make them worse without making them useless. Later flight units really do need to be more attractive from an energy/heat efficiency POV. I also think you can introduce endgame flight units which keep their current poor energy/heat values but have better speed (25 base, -7 additional to about 8 speed?). This allows for a speed specialised build which requires good power and good heat dissipation to run.
Flight options (this is more of a continuous scale than two discrete options but anyway...):
1. Use two slots for flight units, stack mass support utilities and go for a stealth build where you avoid nearly everything and outrun most enemies.
2. Use multiple slots for flight units, use multiple heat sinks and power amplifiers and go for a speed build where you can outrun all enemies.