I've been reading through the book and there's a few rules and things that stuck out to me as incomplete.
The novels describe magical specialization in terms of power and control, and we see the extreme of power with Harry, but we rarely see the extreme of control. The book doesn't really seem to cover what you can do with extreme control either. So what do I do for rules? For example, if I wanted to use air magic to change my clothes in a matter of seconds, or to warp my voice to mimic someone else, or make myself levitate, or to blow the dust off a house of cards without toppling it. Or using Fire magic to set something on fire without burning it. Would this sort of thing add extra shifts to the difficulty of the spell, but not affect the mental stress cost, nor the dangerous consequences from Backlash or Fallout?
We do see some examples -- Luccio's laser is noted as being not as strong as Harry's, but precise and deadly in its own way. Elaine's magic is similarly more control based. I want to say Ramirez's is, too, but I'd have to check the numbers. Justin's trick of setting his hand on fire without harming it or the Bic lighter is definitely control based.
But mostly, it's a style thing. My group tended to interpret high levels of control as, "The spell does exactly what you want it to," like a plasma laser that burns the head of a White Court without harming his hostage.
At some points, Harry spends longer periods of time casting an evocation, in order to make it stronger. Does that count as Thaumaturgy? If so, would you still benefit from Evocation specializations/foci?
Definitely still Evocation, but with a round or two of navel-gazing maneuvers to set it up. I had a player once who, whenever things looked like they were starting toward a fight, would do a "gathering power" maneuver which he would then tag for the first attack.
It strikes me as a bit strange that one of the main differences between channeling/ritual and evocation/thaumaturgy is your ability to take specializations. It seems like that would make Focused Practitioners worse in their area of expertise than a Wizard, which is the opposite of how the book seems to portray things.
One thing to understand about Your Story is it assumes a fairly reserved overall power level for the game. It describes things in terms of 6-10 refresh games, where rolling from a 3 is considered a good roll. A lot of people around here, by contrast, optimize such that rolling from a 3 is considered abysmal.
The game's also written by a Harry who hasn't seen what Morty or Hannah Ascher can really do.
Why can't evocations affect movement? In the novels, Harry uses a spell to make himself jump farther. Is that thaumaturgy somehow, even though there were no circles or props or anything? There's a comment in the rulebook by Harry saying that using magic to jetpack yourself forward would just cause you to smash into obstacles, but why can't you deal with that with sufficient Discipline?
You can. In fact, there's really nothing concrete in the rules stopping you. Harry's comment is more along the lines of, "If you do this, the GM can and should compel consequences for it. It should not be reliable and you shouldn't use the rules to twink your way into flying around like Goku."
There seem to be gaps in Biomancy and what the second law covers. How much can you modify a body, without completely transforming it? Can you make other people prettier? Give them a new face to hide their identity? Restore lost limbs? Change their hands into claws? Give them a second heart?
It's probably unclear here because it's not terribly clear in the novels, either. Off the top of my head, I'd say the danger comes in modifying someone into a different form entirely (turning them into a frog, for instance). A woman with a prettier face is still a woman, and you presumably haven't touched her brain.