I had this question come up with one of my players last week, and at the time I thought the stunt Animal Companion from Spirit of the Century would work as is.
But after reading this discussion, I'm more leaning towards the Item of Power rules for the Wizard PC that wants a familiar, since I was going to have it confer refinement bonuses.
Another PC also has a cat, but as a Pure Mortal, I wouldn't want to hamper him more but losing his +2 Fate Point Bonus, while at the same time gaining the cat's abilities. I think I'm going to use a suggest modified version of the Animal Companion stunt for that character.

Story-wise, I had introduced these two cats in my last Dresden game (pre-official rules), and I had used one of them as a plot device to give a character another clue. One of the cats was adopted from a deceased Sorcerer, and the other was a stray.
Since I'd established these cats as more than just cats, I decided to give them a bit of history and a magical connection. Since Mouse in the Dresden Files is a scion of or an actual Foo Dog, I wanted to call these cats something from folklore too.
The cats are now identified as The Cheshire Cats. Each cat has an associated element from the standard elements in DFRPG.

Crowley - The black cat adopted from a defeated sorcerer is tied to the Spirit Element. Considering its actions in game previously, it is likely to serve a similar role to Bob, if the player picks the communication option from the Animal Companion Stunt.
Boots - An orange tabby with white markings on its hind legs that look like boots, is tied to the Fire element. The PC will be able to use the cat as a focus for fire spells, adding a minimum of +1 to power. Since the cat can be defeated or driven away from a scene, instead of offering the second +1 from Refinement, the cats presence gives another minor mental consequence box. Another consequence is likely more powerful for a spellcaster than another refinement bonus, but I don't see this to be too big a power disbalance. Plus it gives another character I can threaten with the enemies in game.

The Five Element ties for the cats mean there are likely 3 more familiars out there like them, but I think I'm likely to tie them to antagonists, or offer them as a possibility to other practitioner pcs that get made.

Remember, being a descendent of an angel doesn't necessarily make you a good person.

Funny to see the Nephilim pop up in a Dresden RPG context again. One of the big bads of my last Dresdenverse game was an angelic descendant trying to locate a Blackened Denariius. I found it fun to have a group of mercenaries led by this individual who called themselves the Nephilim, and whose insignia was a sword with wings. I intended that to be a clue that this dude might be more than ordinary, as a subtle clue of slightly obscure biblical lore, but I don't think any of my players figured it out.

Perhaps you could add a house rule that Rote spells of below a certain power level, like Lore or Conviction -1, cost one less box of stress? That way Harry can toss around Fuego a few more times in the big fight scenes.