I thought Voyager covered the Doctor's growth from photonic automaton into a full fledged crew member fairly well. To do it, they had to use magic technology from the 29th century and some vague explanations of letting his subroutines loose and able to grow along the way. But that's forgivable.
I do wish they went more into how it was possible he made that transformation, including legitimate emotions and even madness (Latent Image), because that would make his growth into something human-like more believable.
Star Trek is always pretty amusing in the way it takes technological assumptions from then-present-day and projects them hundreds of years into the future. Potentially dangerous nebula that needs to be charted? Put some high ranking bridge officers in a shuttle and get them out there! No need for a remote piloting or even an autonomous probe (something they have and use from time to time, when the writers remember). Unwillingness to acknowledge the potential of autonomous AI (except when it's weak, harmless, or confined to a human-like body) and the aversion to self-chosen evolution are other examples of this.
It's interesting, maybe lazy, that between TNG and Enterprise they kept the progenitor character of the most advanced androids and the progenitor of the genetically engineered humans in the same family line. But at least it was an excuse to get Brent Spiner back on screen.