Well, in most of my experience*, thrown weapons are more like backup weapons when the “real” weapons won’t do the trick.
Keep in mind that recent D&D didn’t intended to balance thrown weapons against other major styles, and simply the designers never bothered making them better.
Which is a terrible mistake: thrown weapons are cool and not-totally-ridiculous, so they should efficient, although in their own way. Honestly, I don’t care about their real-world efficiency.
Which brings me to the question: what do you want thrown weapons to do? They should be efficient ranged weapons, but they shouldn’t be exactly like bows, crossbows, guns, etc**. They should have a unique feature, and other disadvantages to counterbalance it. Think: It’s the damage? The range? The ability score unusual to ranged weapons? The number of attacks used? There’s a lot to think here. Once you decide it, you can effectively re-design thrown weapons.
*There’s one exception: as I’m reading AD&D 2nd edition core rules, if you make a single-classed Fighter, with high strength bonus (exceptional strength, that is) and specialize in either throwing daggers or darts (other weapons won’t do the trick), you actually get a very high damage output; completely broken. I don’t know about the splatbooks yet, but fixing this is one of very few house-rules that I’ll adopt in my game even if I’m just testing it.
**My first try on making guns made them too much similar to already existing ranged weapons. That must have been one of the factors why that, despite being balanced, almost no-one was interested in using them.