The Shadowrun Companion has me looking at SR6 again.
That's the highest praise I hoped for. Glad you like it!
...
From what I can tell from some rolling dice, there's no mechanical incentive to use a single target combat spell over a gun right now -- in fact it's the worse choice from a gameplay perspective. That doesn't feel right to me...
So a few things:
Direct Combat spells resist with dice pools that are harder to augment: Will + Intuition is going to be lower than Reaction + intuition, at least on combat types anyway.
Direct Combat spells have no soak. Net hits are additional damage. Full stop.
Indirect Combat spells might be more of a wash on the resist pool, but the dynamic can be flipped. Big brain archetypes might have great Will and Intuition, but making them sub in Reaction can be a form of "penalty", depending on your target. Different tools work better for different jobs, chummer!
Indirect Combat spells are then soaked, yes, but then again so is damage dealt via guns. I'm not sure what the 'triple' defense pool you're speaking of is coming from. Are you talking about counterspelling? If so, consider that's much rarer to encounter than the target spending a minor action to dodge.
Smart samurai don't cash in 4 minors to attack a second time; they dodge everything coming their way. Guess what you can't dodge? Spells. Not even indirect combat spells.
Of course, FA is borrowing the indirect combat area attack mechanic, so the two are fairly comparable. While guns don't have drain, you DO chew through ammo furiously, which may as well be comparable to drain when it comes to sustaining the attacks. Also note that area combat spells don't have an AR penalty. So where the FA attack is almost assuredly not generating Edge (from AR at least) the spell suffers no comparable penalty here. And, the actual area is twice what a FA attack generates.
There's also factors outside the raw dice mechanics. You can carry your capability to cast spells through MAD/MMW detectors. Even through wards/mana barriers for that manner, unless you insist on keeping quickened or sustained spells. Spells have drain rather than ammunition, sure, but explosives are nearly impossible to slip past a chemsniffer, and guns are pretty bad without ammo. Spells leave astral signatures which can be as much of a PITA as spent shell casings going everywhere from a gun, but at least DURING combat spells aren't hugely loud BANG BOOM BANGS for the whole neighborhood to hear. Even silencers don't do much to quiet guns when potential observers are nearby.
Some additional factors in favor of direct combat spells: you can "shoot" someone around a corner by viewing their reflection in a mirror. You can "shoot" them through glass too, without breaking the glass.
Anyway. If nothing above is persuading you, absolutely nothing's stopping you from house ruling that combat spells get a free Amp Up adjustment or whatever
Edit: Another point specific to 6e... don't forget that in this edition you can spend Edge to heal. You'll be more likely to suffer drain in this edition, yes, but you can heal it more readily than before, too.