Regarding the skill level of attackers:
Historically, I believe that most real-world armies from the Dwarf Fortress period consisted of unskilled conscripts -- farmers who were forced to join, but who had little or no experience with weapons or fighting.
There were exceptions, of course (the roman legions, etc), but those are the exception and not the rule, and the reason they did so well was precisely because they were professionals going up against unskilled peasants. They required huge empires supporting them that most people just didn't have. A few other countries would train absolutely everyone for the military (the English requirement that everyone train in using the longbow, all of Spartan society), but that, again, was because professional armies were so rare -- most armies were, largely, just peasants who the local leader forced to pick up weapons, augmented by maybe a few mercenaries and the like.
So having most invaders come down to little more than unskilled peasants is actually not all that strange... and if the player implements a modern-style military with extensive training for conscripts that compose a significant portion of their population, the fact that they will brutally slaughter those invaders is based on historical fact.
Remember that the player views things as a game; they raise and train an absurdly large army compared to what is realistic. In the real world, very few societies from the tech level Dwarf Fortress is at are going to turn a huge chunk of their population into a dedicated military that spends all their time training. (And those few are going to be legendary for their outlandishly militaristic culture.)
Most societies couldn't afford to have that many people as dedicated fighters -- farming was too important and too time-consuming. If you want to keep the player from training up huge armies of uber-legendaries that slaughter any invaders, I think that the best approach is to try and make it more difficult and less viable for the player to have such an unrealistically big military focus -- not to try and give everyone that same absurd amount of training.
OTOH players should be able to play Dwarven Sparta if they want, of course.