This is probably a stupid question, but for big name shows why couldn't ticket providers print the buyer's name on the ticket and then label any extra tickets they buy as guest? When you enter the venue, you have to show ID showing it is actually you and then if you buy any extra tickets label them as guest tickets? It wouldn't solve everything, but scalpers would be more reluctant to buy a ticket if they know one of their tickets can only be used on themselves.
This is exactly what Nine Inch Nails used to do with their fanclub, and it was a great system. It is probably a little labor-intensive to think it could be done for all the seating, though.
There is also the paperless ticketing system that Springsteen and ACDC used which is another good option. It doesn't make scalping impossible, but makes it much harder.
Seth, you have come out as saying you are against scalping. Well, this might be your chance to do something about it. Instead of having TicketFly scramble to increase capacity for demand that was largely driven by scalpers, why not institute a system for big shows that seriously curbs the scalping. It might even cost less to do that than to do the needed upgrades to TicketFly.
It is worth noting that the TicketFly system worked fine for MMJ. I think it is just a matter of handling that initial period of very high demand. So, handle that high demand period in a different way that has the added bonus of getting the tix to the real fans and not the scalpers.