Maybe I'm reading you wrong, but it sounds like your simultaneously think the system is too weak (want additional bonuses for charging) and too strong (limit the damage bonus)...
I agree with the latter point: Adding agility as damage in yet another way is a dangerous road to take. It's already risky to have it on weapons, potentially allowing for strength to be a dump stat. I do like that the damage bonus relates to the charge distance, though... maybe it could just be capped at 4, but otherwise work as-is?
+3 or +4 is certainly less than an existing wound. But why should it be more than that? We're talking about free bonus damage on an action you'd probably do anyway (movement).
Besides, I think you're underestimating that damage boost. An average Joe (Sb 3, Ab 3 with a Sword) charging another average Joe (Tb 3, AP 3) will have a 100% chance of inflicting a wound, assuming he hits. If he hadn't charged, that chance would be 80%. That's a noticable difference, and it obviously scales to be more an more worthwhile against tougher opponents.
It's also worth noting that many of the wound chart effects come in sets of 3 (ie. Wound x causes effect A; Wound x+1 causes effect A but with a harder test, Wound x+2 causes effect A but with an even harder test). Boosting your damage by 3 will almost always move you to the next "tier" of wound effects, which is often a big deal.
Finally (this is turning into a long post - sorry), your example:
Of course charge looks bad when you make a high-risk maneuver and then fail the roll. That's the same as saying that the opponent then spends all 4 AP to attack back, but rolls a 99. Whoops - big advantage goes back to the first character.
No action should be the default in every situation. Charge shines in some cases and is a bad decision in others - you chose a very bad one for your example.
I am saying that bonus-based modifiers generally scale badly.
And why is the risk for the charge greater than for the charged? That's the point. You seem to think it balances out. I think more AP > damage bonus (unless very high Ab).
Kind of takes away from any tactical decision on weighing up whether it is better to make a controlled, skilled attack (multi-hits) or a powerful charge. I like having pros and cons to different approaches. Someone is going to have to remind me what the actual problem is with the existing Charge rules because I don't see it.
It is a continuing problem in DH2. To be precise: a charge carries a risk for both parties because of the higher energy on impact. Again, it's in error to model it so that the defender gets to respond to a charge with a flurry of attacks instead.
Even so I think the benefit of multiple AP outweighs a bonus to attack except at high Ab levels.
If it's better to be charged than to charge... that's wrong.
Alex