interestingly enough, when muskets started coming up, for a certain transition period, one could get paid much better as a soldier if one could operate a bow: further reach, better accuracy, better firing rate, more damage, etc.
muskets were used because having an army of musketeers requires much less training. The resulting armies were not necessarily better than an army of bowmen or macemen.
But instead of training your soldiers for years on how to effectively use a bow, you could simply recruit and "train" your soldiers in a matter of months.
The training ( also, later, of early riflemen ) consisted of a lot more drill and discipline than of actually shooting - it was more important not to break ranks than to shoot well as the guns were inaccurate anyway and whoever got closer to the enemy when shooting had the advantage.
In conclusion, I think making the musketmen only slightly stronger is absolutely fine.
CR is probably meant to negate city bonusses, which musketmen are not up against - but, if you do bombard, it is true that macemen are better attacking a city.
In close combat ( as conquering a city tends to be ) this may be justified. But I think that has been discussed sufficiently already