As it stands, there's no reason to use Throwing Axes over Javelins as a skirmisher. Javelins can more often than not two shot people, have a better throwing arc (AKA can be thrown reliably at longer distances), and can deal with multiple people semi-reliably (stabs go through targets).
How does Throwing Axe stack up? Throwing Axes have one more ammo capacity (6 for Throwing Axes and 5 for Javelins) and are generally faster (can be thrown faster and swung faster). They're basically worse Javelins with worse damage and range with nothing significant to compensate. The design philosophy behind Throwing Axes is that it has shorter range for a much faster throwing speed. The only problem is that the distance that you need to be to perform well with them means you're much more vulnerable to combatants. There's a cooldown period between throwing a weapon and being able to guard. Throwing axes throw faster than Javelins but it still takes a significant amount of time to have your block back up.
My two suggestions to buff Throwing Axes would be:
-Buff Ammo Capacity (maybe 8 instead of 6)
-Reduce the cooldown period between throwing and blocking
-Reduce the stamina cost of throwing
This would significantly differentiate the Axes from the Javelins by strengthening the idea of them being "Weaker Javelins that are faster" without having to directly nerf Javelins.