I dunno, it's hard for me to think of ideas... with the Medic upgrades, I think they were nicely balanced changes, things that just tweaked the way the class works or gave you options, but not so much as to change the medics play style completely or role in the game, cover up his weaknesses or power up the strengths.
The Pyro's been a mixed bag. The flare gun was a nice add, giving him a *little* range, but really only good if the Pyro has good aim or the opponent is standing still, and doesn't completely replace the shotgun (it's still better for finishing off an immolated opponent). The new axe = whatever. The air blast is alright and has been a thorn in my side (being a demo man mainly) so I haven't quite decided on whether it's a major game changer. I hate the back burner though, that one is a definite issue for me. Pyros were problems to begin with in 2Fort, now they totally dominate it.
For the Heavy...I dunno, I think the class already does perfectly what it's meant to do. Again, whatever the changes are, shouldn't "fix" a weakness or over-boost a strength. (Side: that's why I disagree with giving Sniper's something to save them from people who sneak up on 'em; the Sniper's weakness up close balances his strength at a distance) It should just give the player some options in how they play the role offensively or defensively.
The Heavy's main function is to stop the offense: just sit there, clog up a doorway, eat damage and spew bullets. Some thing that perhaps boosts a Heavy's health for last ditch attempts to stop a rush would be fitting, like some kind of adrenaline overdrive that gives the heavy a bonus 150 health but after 5 seconds subtracts 100 health. (This would be an ability that would need to be charged up.)
An alternate machine gun that had a more focused cone of fire but no ability to move (or maybe some pushback) would give an offensive Heavy something to do against a distant sentry placement. Or maybe a hyper-spin gun: Rate of fire is doubled, you get a slight ammo boost but the Heavy can't move when firing, only aim.
I think Gerbil suggested some kind of teammate throw ability, which I think was neat but too much of a game changer/griefer magnet. But we do need to come up with something for the Heavy to do with his fists, his brute strength and the bullet chain wrapped over his shoulder. Maybe the Heavy could become a walking ammo despenser, but I think that's something more for NGs. Maybe a bear hug attack?

Weaker than a punch, but it immobilizes an opponent unless they can shake out of it. Or maybe a Zangief style windmill attack, or Hulk-like ground smash, the upshot being that it pushes or punishes enemies that get too close. (I'm looking at you, pesky circle strafing Scout)
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I don't necessarily think that the Heavy is underplayed, I think it's more that a team really *only* needs one, or at most two Heavies. Any more than that and you start to weaken your ability to get to CPs on time, run the flag, remove sentries, etc. You can always use more of everything else though (Pyros, Scouts, Soldiers, etc.) and not get penalized, but going overboard with the Heavy has consequences.