So your problem actually has nothing to do with +2 stress stunts and everything to do with stunts that reward specializing in a specific weapon?

That's not how I'd read that - I don't think he dislikes the notion of rewarding specialization, just that he thinks it's not on its own enough justification for a maximum-normal-power stunt.  So, for example, I think he'd probably be ok with a stunt like:

Hammer Blows: deal an extra +2 stress on a hit, when wielding a two-handed war hammer, in a situation where you have plenty of room to swing your weapon unimpeded - this last condition may require (or be countered by) appropriate declarations or maneuvers, such as "paper walls" (to get room to swing in the otherwise tight corridors of a japanese style palace), or "knife-fighting range" (as an example of a maneuver someone else could try to use to counteract this stunt.)

Any Mortal stunt that is a straight modifier is a +2 modifier on a single trapping.

Except for attacks - which is one of the things evocation can do.  (Plus not being quite a single trapping per se, as you mention.)

She's pretty set on being a 'Lightning "focused' practitioner".  I even suggested she could go "air" or "earth" as per the books suggestions, but her response was, "Whatever, I'm only going to cast lightning spells, so it doesn't matter."  So while ball lightning sounds awesome, I don't think she'll go for having a sponsor.

Well, the thing is, Kemmlerian Necromancy, despite being listed as a sponsored magic in terms of game mechanics, isn't really attached to a sponsor; it's more of a "I can do nifty things with death magic because I'm really good at it" power - which is why I suggested it as a basis.  It's not even clear if you can take sponsor debt with it - and totally up to the GM what form a compel on a point of sponsor debt would take...

This is what I'm trying to avoid.  Other than that I'm trying to let her do what she wants, and let her put refresh in other areas.

Fair enough.  In that case, I'd suggest sticking to "these are the rules", and simply state that you're not comfortable with homebrew powers to start with.  Suggest that maybe such things could be considered later - especially if her character manages to find an in-game source of knowledge or power.  Heck, a quest for power can be a potentially pretty strong motivator for a character; that could be a great aspect to drive plot.  "Oh, someone stole something from the exhibit on ancient greek artifacts?  Yeah, we'd better look into that.  Uh, and, yes, return it to the museum, of course.  Once we're done with whatever it is.  Sure."

On the one hand, there is certainly some can-of-worms potential, as pointed out by UmbraLux.

On the other hand, for what you're doing, that probably doesn't matter.  See, the only time you'll run into problems is if someone starts trying to hunt high numbers to the exclusion of all else - and that's really a meta-game problem.  I'd suggest allowing such a thing, with the caveat that you may want to change it later, after seeing how it works in play.  (And, given the high power of spellcasters in general, you may very well want to change it later, even if it's "balanced" against someone with evocation.)

That said, there are a number of ways to boost lightning magic without actually buying up specializations.

I'd start by looking at Kemmlerian Necromancy; a Lightning Mastery "sponsored magic" based on that would give her the go-ahead to do all sorts of fancy things with lightning evocations (turning on lights, ball lightning, etc), above and beyond the normal evocation attack / block / maneuver options.

I'd also look into Breath Weapon (though with the note that it's probably overpriced - at a minimum, I'd switch it to running off of discipline or conviction rather than weapons), to give the character some ability to throw lightning around without mental stress.

And, third, I'd look at Evocation again.  Ok, your powers are all lightning / electric based.  That could give you some access to Air, Earth, and Spirit - lightning itself, plus some ability to manipulate weather / wind, plus magnetic effects (telekinesis vs. metals), plus some mirages & illusions (deflecting light by heating the air, creating light), etc.  And if you run into a situation where your particular focus limits you more than evocation would?  Well, that's a perfect time to suggest a self-compel to the GM...

Actually, what would fill the gap for partial changes is the -0 power Human Guise (instead of the +1 Human Form).

In other words, you need more shifts of power than the defender's skill roll.

Not how I read that.  RAW, you need shifts of power equal to or greater than the target's (unrolled) skill.  An evocation maneuver only gets dice involved for control - or no dice at all if it's a rote.

I'm somewhat inclined to houserule changes to that for my game, but haven't worked out exactly what houserules I actually want to use.

As a general rule, I assume that a spent fate point / tag / whatever has to do something.  If someone tries to spend a fate point but would still miss, I let them know, and give them the option of either having the point refunded, or spending more points to hit.  I'll also refund a fate point if someone would have taken out the target without it.

The exception to this is if the defender also has fate points or tags to spend.  If you miss by one, spend a fate point to hit, and then the defender spends a fate point to be able to dodge - both fate points are gone.

Magical maneuvers are a wonky thing, though, since it's a set power against some (un-rolled!) defensive skill.  In this case, I'd typically tell a player outright "You're going to need a power 7 effect to hit this guy with your maneuver-that's-defended-by-athletics" - or, at worst, allow the PC to roll an assessment as a free action to know the right power value.  In the latter case, I could see allowing someone to eat backlash to get off a spell that can't work even at its best, if they failed that assessment.

Link, please?  I do frequent said spoiler board, and also remember no such consensus.

Edit: Not that that necessarily has much bearing on your game - if, in your game, uberghouls are outsiders, then that's what they are.  But I don't think it's really a good default assumption.

I'd go with Silverblaze's suggestion, cost it at +2 as a power, and add the limitation that you only get the bonus when in a situation that is clearly in keeping with the weapon's agenda.  Even the swords of the cross don't grant their +1 weapons all the time.