This really is just a wild guess with no substential facts backing it, so take it with a grain of salt. But I think militias would probably be the precursors of standing conscript armies, as opposed to low ranking nobles and peasants.
A militia would be outfitted and trained by the community, and even if they would only be what we now call reserves, this seems to be a better context to develop more advanced and professional organization.
If a rich city like Bern, Zurich, or Prague is outfitting its entire militia, they can order weapons and armor in bulk and pay for it from the defense budget. Not sure how it was for knights at that time, but the popular image is that of each knight being responsible for the training and equipment of his lance of six to eight men, and having to pay for it with his own funds. That probably would make armies of knights look a lot more ragtag, and wouldn't lead to a lot of training in large unit tactics. And I think both the Swiss and the Czechs were quite famous for their exceptional use of large cohesive units. Quite similar to what made the Roman legions great.
Also, militias are defending their home or at least fighting battles so a shared enemy never makes it to their own home if they can stop them in an allies territory. Knights and their men would be fighting because their lord had some political ambitions or even just for pay if they were freelancers.