I've long toyed with the idea of making a Dresden mod for certain games, like Shadowrun, or even a full on RPGmaker game. It definitely can be done, but it would need several things to be, you know, good.
1. A combat system that reflects the Dresden Files' lean toward ingenuity. Fights with common mooks should be less difficult than with, say, Cowl, but should still be threatening; Harry has most often come close to death from simple means, and a gun works just as well as an storm-driven-exploding-heart-spell. Better, usually. I normally prefer some kind of turn-based combat, but I think a nuanced real-time system would work better for Dresden to represent the way Harry actually fights. Closer to the first Dragon Age's soft-pause system, but not quite the same, if anyone's familiar.
2. There's no doubt in my mind that the genre should be a noir-style investigative RPG. Borrow some of the elements from the last few Persona games concerning time management. There should be cases available on certain dates, and the time in between those cases can be useful or a waste as you see fit. You can spend time with your friends, or spend time pursuing side jobs to earn extra money (and yeah, I actually think that the first part of the game should be heavily concerned with Harry making rent). You can spend time brewing potions, enhancing gear or making new gear, et cetera—but the salient point is that time is limited, and a zero-sum situation.
A standard type of level advancement function would work pretty well. Harry learns how to better use fire magic (for use in the big missions), or better tracking spells (to save time with side missions, or increase the reward for their completion), or whatever. But Harry himself should never get larger amounts of health; he's as squishy as ever. He just gets better at using his shield (or makes a better shield), or enhances his duster, or something like that—ways to avoid damage, but a bullet is still a bullet.
Investigations for side missions shouldn't take much longer than a day or two of in-game time (which I say should be based on a scale of taking between 3 minutes and an hour, depending on if you just craft or rest, or you participate in some activity). I think the side missions should range in difficulty, and require actual thought rather than "go to point A and bring me XYZ." I think they should be closer to logic puzzles—someone asks you to find out who stole their wedding ring, for example. You have options on how to figure that out. You can try tracking spells, investigating with standard means (interrogating witnesses, canvassing, bribing a few street people in the area), et cetera. But you still have to correlate all of the data you gather to correctly identify the culprit.**(I have a built-in shortcut, but it's better related to a different point for later).
The Big Missions, which I'd take to involve the events of the books, should be several-in-game-day-long affairs, and involve a mix of problem-solving, combat, and teamwork with your allies. Knowledge of the book should help, but I think that it'd be better if the game still required you to play the events straight—you can know without a doubt that Victor Sells is the Shadowman, but you've gotta provide evidence, which means you still have to investigate.
If they paced it like Persona 5, there'd be about a month of downtime between getting Big Missions. It'd mess with the timeline of the books, but whatever, I'm okay with it.
Side note: you should be able to get side missions from the Wardens, or other factions you sign up with, which all incur some benefits at some kind of opportunity cost.
3. A Karma Meter would add a new vector to things. Harry is constantly being offered deals. A video game is a great way to provide Alternate Universe stories in which Harry can choose to accept them. The first time Mab offers him the Winter Knight job, you should be able to take it. It would shift your karma meter towards the darker side, but offer new, powerful abilities and resources. Ditto with signing up with the Wardens, which would shift it toward Neutral (cuz I don't consider them to be "Good"), or the Brotherhood of St. Giles, or Marcone's Legitimate Business Interests, or Lara's Totally Not a Sex Cult, I Pinky Swear.
Other things that affect the karma meter are solving side missions in ways that follow your code. Opposing actions (doing Dark Things when you're currently in the Light Things side) should only be able to shift you toward Neutral, not tip you over the scale—that should be reserved for the next paragraph. But doing things in accordance with your current standing should reinforce it—a Dark Harry who does Dark Things should get Darker. The idea is to provide a viable Neutral pathway; most games are Black and White, and your choices are either "set this orphanage on fire" or "donate your kidney to a stranger," so I think a way to play neutrally would be cool.
Black magic and making deals with Bad Dudes should tilt your meter towards the Dark end of the spectrum. **(relevant to previous point); you should be able to summon demons as an information source, for example. Summon up a demon, make a deal, and bam, your side mission is instantly solved, at the cost of shifting toward Dark. Save yourself some time for those who want to blitz through the game or who find the mission too difficult, but risk making enemies of the Wardens and the White Council. Shift yourself too far in either direction, and you lose certain allies; if you're, say, 75% dark, Michael won't help you anymore; if you're 75% light, Nicodemus is locked out permanently.
There should also be some benefit to playing in any particular way; the darker you are, the more you can abuse magic, because you don't really care much. So Necromancy can become an option, along with insta-kill magic, mind domination, et cetera. But the Lighter you are, the more you can hang out in public (cuz the Wardens will like you, and so will the police), and the more allies you can bring along, and the better you are at the softer magics (like item creation, access to Soulfire, et cetera). Neutral paths should provide a mix of benefits; you have access to most allies, and can invest your experience in either end of the spectrum, but you lose out on the benefits of going 100% in either of the other two sides.
4. I think that story missions should be locked out or altered based on the above karma (I'm only using that term because of previous gaming conventions) thing. If Harry is the Winter Knight, Small Favor becomes different. Ditto if he's in bed (metaphorically) with Lara's faction during Turn Coat. If Harry picks up a Coin during a Death Masks mission, and joins up with Nicodemus, then he can be on the other side of events of Small Favor. If he's way into black magic, then Dead Beat might be about the Wardens looking for him.
5. The different factions should provide extensive differences in the game's experience. One of my favorite games in the last decade was Kingdoms of Amalur, that boondoggle that will never get a sequel thanks to the state of Rhode Island and Curt Schilling (seriously look into how stupid the whole thing was if you want, it's a real roller coaster). There were a ton of factions in that game, and each had their own questlines. I think something like that would be cool, but in a different way. You can only participate with factions that work with your current alignment, first of all. So groups like the Wardens, the Brotherhood of St. Giles, the Knights of the Cross, and the White Council might provide you with optional side quests, like "Hey, I think there's a Red Court nest operating out of this club—check it out, and take them down if you can," with unique and interesting rewards. Those quests can affect your karma alongside your standing with the faction, and as you increase favorability with a faction, different benefits open up. New allies for certain missions can be unlocked, along with new experience progression paths—I bet the Brotherhood of St. Giles has a lot to say about mundane things, like gunplay and lockpicking, while the White Council could probably teach Dresden how to blow things up more efficiently, while the Denarians can teach Harry new elements to his battle-shifting capabilities and different applications of Hellfire.
6. The voice acting in this game, along with the animation quality, should be on par with Uncharted. I remember how blown away I was at the depth of expression from the cutscenes in the first Uncharted game, which I picked up the day I bought a PS3 back in...2008? 2009? Whatever. It was freaking superb, and it's only gotten better. Dresden deserves the Triple A treatment, dang it.
Obviously, if the game was this expansive, there's no way you could cover the whole series up to now in one shot. It'd have to be a series of installments, and I'd be just fine with that (so long as you could maintain progression between games, like Mass Effect). Honestly, I think a game like the above would be insanely difficult to make (which is why I haven't made it myself, plus, you know, I don't want to get sued), but would have so much mainstream appeal that it'd be hard for it to fail.
One of my biggest concerns is that we'd get a Dresden game, but it'd just be a ripoff of The Wolf Among Us. I don't want Quicktime events and dialog trees as my whole game, darn it. I don't want quicktime events at all, for that matter.
Anyway, this is how I'd do what I consider a good Dresden game. Alas, t'will likely never happen.