In VOY "Emanations", the EMH has no trouble replicating working neural tissue. In DS9 "Rivals", the El-Aurian con artist not only manages to get copies of alien technology from the Cardassian replicators, he gets scaled-up copies. Clearly, the replicators can achieve significant feats when they are pressed hard enough.
It's probably just a question of allocating resources. Most replicators might be capable of extreme resolution in terms of their hardware, but practical resolution would be limited because a) it saves computational resources and b) the user has no need for better resolution in the general case. There could be hardware limitations, too, but those probably have more to do with size/output than with resolution - that's where industrial replicators would come in.
I have no problem with the idea that replicators normally
work on "molecular resolution", as long as that's enough to resolve the molecules that make up the all-important taste of food. That doesn't mean the replicators couldn't handle better resolution with proper keypresses or with proper tampering of their innards.