I have to say I really didn't care much for the heavy weapons. They slow me down (or at least seem to) while offering comparable (or slightly less) damage per shot than their normal weapon equivalents. To be honest, I'd rather see some kind of "Set up" and "Tear Down" mechanic and take accuracy/damage/whatever penalties (heck, I'd settle for not being able to fire). Then you can put in Terminator Armor or something and make all heavy weapons automatically set up, if that's really your thing. But in general I don't want to carry a weapon that slows me down, especially in a level where I end up backtracking a lot--I'm wasting time between packs of enemies.

I think that Heavy Weapons should be specialized for specific situations, and do the job in those situations well, falling off elsewhere pretty hard. They should combine large clips and long reload times--you don't want to run out of ammo in the middle of a fight. 

For instance:

The Heavy Flamer should be your go-to anti-horde weapon, but fall off rapidly as enemy armor increases.

The Heavy Bolter should work well against infantry, especially ones with some armor, but lose to really large hordes or a few armored enemies due to a large clip size. 

The Plasma Cannon should emphasize its anti-armor damage and blast radius, focusing less on rate of fire and more AoE attacks, especially ones with 50% armor pen. However, due to its "gets hot" special rule, if you're fighting a horde you can quickly find yourself without a gun.

The Multi-Melta should be a primary anti-armor weapon, with high damage. All of its attacks should ignore armor, but it should compensate with worse range and more heat generated.

This clearly separates out the role of each heavy weapon, and adds in tradeoffs that might be offset by mission type. Are you going to have to kill Dreadnoughts? The multi-melta makes a lot of sense. Are there tons of hordes? The Flamer might be your thing. Are you fighting Chaos Space Marines? Plasma cannon, definitely. However, you'll find that whatever other weapons you take need to counter for the problems with your heavy weapon. If you take a Heavy Bolter or Heavy Flamer, you're going to need something else to deal with that Dreadnought, and also heavy infantry. You could take a heavy flamer and a Multi-Melta, but run into trouble for enemies in the middle of the spectrum.

I feel like a lot of complaints for the heavy bolter come from teh fact peopel don't use the shift key which is 100% mandatory if you want to get any use out of the left and right click. Once i discovered this I found the weapon amazing.