I do agree with this. What it does, is that it opens up for more invididual leadership style gameplay. Meaning if one takes a more negotiating style, the enemy may also be more open for deserting or perhaps bribery. In different degrees as well - meaning, if the battle goes bad for the enemy, they may offer to become prisoners at an earlier stage in the battle.
And if one takes a harder line, one's own mercs may also be more susceptible to the same things, because one puts them in unnecessary risk, so the motivation to give up becomes a bigger factor. Maybe even giving the entire team a hidden conscience of their own, meaning one does not have 100% control over them. If a lot of them becomes wounded, they may revolt and desert to the enemy either as prisoners or maybe even as hired mercs working for the enemy. This could be connected to the difficulty degree one has chosen.
This would bring an entirely new element to the game that i think would fit in with the genre. It is in line with reality as well.
In JA2, this was hardly a factor. The enemy very rarely ran away, and only with perhaps one or two mercs remaining. And they would only offer to surrender if one had one or two mercs left oneself. There could be a wider degree of this in JA3.