I think there are two big problems with throwing weapons:
A) You can carry WAYY too many. When was the last time you heard of someone carrying 20 Axes, or 30 Javelins? Seeing as people normally carry two or more stacks of throwing weapons, 2-4 should be more than enough ammo for a stack.
B) What you do carry is too light, allowing players carrying huge loads of throwing weapons to still run away easily.
I wouldn't mind damage being upped slightly, if weight were upped, and the amount of ammo reduced significantly. I think this would make the game more fun for all.
Literally everyone carries throwing weapons. Combine that with those who play as archers, and it is almost impossible to use any kind of two handed weapon, or for-go carrying a shield. Furthermore, when you do get in close combat with someone, you'll more than likely receive a spear/axe/arrow/bolt in your back than getting hit by the other guy's sword.
[Edit] Also, I don't think that throwing weapons should be standard(free) for non-ranged infantry. Only skirmishers really carried such weapons. In M&B, there's always been an over-dominance of ranged weapons -- even in single player. The only difference is that CPU's can't aim, or be cheap. However, players can. So this imbalance is brought out strongly online.