Very interesting question, pardon me if I write a short essay
From what I've read, a lot of really basic stuff is overlooked in an underground setting. Roughly speaking, the five basic needs of life are: food, water, oxygen, living space, and appropriate temperature. I've yet to see an underground culture developed that really accounts for all five of those (though to be honest it's rare to see them fully developed, and there's a good chance I've missed some that do consider that kind of thing). It'd make sense to at least consider how those five things would influence the way the city would develop, since they really are important.
(Note: the below is based on the few underground civilisations I've encountered, hopefully someone can point to some that actually do account for these, since that'd be well thought out fantasy that I'd like to read!)
Food
Most of the time the food source isn't even considered, even in the case of your typical dwarves shunning everyone else and living deep underground. They often seem to eat a lot of meat - where does it come from? Do they have the equivalent of underground factory farms (since space would be at a premium)? Where do they get the feed from? Where do they get their own vegetables, since pseudohumans presumably need the same nutrients humans do in real life, which cannot be provided by meat alone. Do they farm fungi (and if so, what do the fungi consume)? If all food is brought in/traded from outside, then can it truly be considered an underground civilisation rather than an outpost of a larger civilisation?
Water
This the easiest to account for thanks to underground rivers, though it'd also be nice to also see references to rainwater filtered through the rocks. Water collectors built underneath stalactites would be a pretty cool detail. You could also cut wells down to the water table.
Oxygen
Another one that doesn't seem to be considered, there really does need to be some reliable ventilation. This bit reminds me of ants and termites - they create brilliant ventilation systems to manage the oxygen and carbon dioxide levels so both they and their farmed fungi can survive indefinitely. You'd have to design your architecture so that the air can flow through properly, circulating the air and keeping it fresh. Some modern buildings do this passively, so they'd be a good place to start looking at to see how this could be done.
Living Space
As you said, this could be planned out in advance, particularly because weakening the structure of one area could bring the whole thing down. It'd make sense for the plan to be constructed in stages, with various sections being planned well in advance and then excavated when the extra capacity is needed. However it could still be grown as per normal cities - and then you'd be able to add a third dimension to the growth, allowing connected infrastructure to cluster together more closely. I think the routes goods travel would be influenced by that - carrying heavy stuff upstairs all the time would be a nightmare, so a well organised city would arrange things so that goods tended to travel downhill or stay on the same level.
Temperature
Another thing that's often ignored - beyond the influence of the sun it's cold, until you get reeeally far down. If you're using big fires to keep the temperature up, where does the fuel come from, and how do you deal with the smoke?
The obvious solution to all of those problems is magic, but I think that would be kinda lame...
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