I'm replaying the Hegemony after some pause, but I could not find the discussion we had about this topic some time back, in particular if it's somehow possible to adjust in some configuration file possibility to train non-native units again. I think I recall such discussion, and I think the answer was that it could be done but not specifically for allied and mercenary units but only both, however I'm not sure if it's not a wishful thinking.
The thing is, playing late game, I would like to use also other units, for different styles and such, but if they can't level up to get bit better (still worse than leveled native units) there is no point to use them, because they rout so fast and eat so much. I think it's offset enough that their base morale is worse (allies) and both base morale and cost is worse(mercenaries).
I also think it would be more of fun.
I don't generally have problem with recruits in late games, so I don't think it's too prone to exploiting. But to have few Thessalian cavalry units with me that can get practical would be both great for role playing, historicity as well as pure fun. Plus, having those extra peltasts from agrianes and amphotycon phalanx is pretty much useless when they can't level up... And it makes no sense.

The thing is, playing late game, I would like to use also other units, for different styles and such, but if they can't level up to get bit better (still worse than leveled native units) there is no point to use them, because they rout so fast and eat so much. I think it's offset enough that their base morale is worse (allies) and both base morale and cost is worse(mercenaries).
What sort of gets me is, well. Eg: on my Athenian game.

Theban hoplites fight with Attack 160 and Def 100, the Athenian ones with Attach 150, Def 100. Not so bad.

But the Thebans have 80 missile def and 50 men, the athenians have only 60 missile def and 40 men. Though levelling can help with the food problem there are logistics ways to deal with that. Having your Hoplites get destroyed by AI's Thracian peltast spam is somewhat more annoying. With a decent general they get a decent enough logistics/heroics. (Logistics also has diminishing returns apparently so not getting the unit all the way to 5 logistics isn't only annoying but doesn't help that much). The basic stats don't change, except for morale. But usually even the merc hoplites don't really break that much, plus at 50 men, they are a bit harder to overwhelm.

I used the Thebans early on for dangerous assaults. They were so good at it and better at it than the low level Athenians that I gave them the top generals and just had at it with a couple of them, along with uberelite Messianian unit.

only way i know of is with console commands using the addbrigade command in the console.