I've been looking at this as part of research for Lane v. Holder and Dearth v. Holder. The short of it is that when the GCA of '68 was passed, there was no NICS. In fact there wasn't much of any federal law concerning handguns at all (the GCA was the first big piece of federal legislation for handguns, and the biggest since the NFA). In the interest of making whatever regulations the States wanted to enact stick, the Feds invoked their Commerce Clause powers and regulated interstate transfer of handguns and long guns. The long gun restriction (allowed only between a seller and buyer from contiguous states) was eventually removed, but citing "pressing concerns about handgun violence" the handgun transfer ban remains.
The FFL is responsible for making sure the purchase is legal in the state in which they do business. That was true in 68 and it's true now; if it turns out an FFL sold a gun to a prohibited person, or in violation of state or federal laws, the feds will go over their books with a microscope, and if there's any evidence the FFL knew, or should have known, they were making an illegal sale, revocation of the FFL is the least of the seller's worries.
The two-FFL system thus has one significant remaining value; the removal of responsibility of the FFL holder to know when an out-of-state purchase is legal and when it isn't. The FFL selling the weapon is in effect "selling" the weapon to the end buyer's FFL, who then resells it to the buyer. That's what the bound books will look like regardless of exactly how the money changes hands. Selling a firearm to another FFL is always legal regardless of how many state lines it crosses. Thus, responsibility for the final transfer to the end buyer ends up in the hands of someone in the buyer's home state, who *should* know the laws of that state as well as federal laws.
That being said...
There are two cases currently working their way through Fourth Circuit. The first is Dearth v. Holder; Stephen Dearth, a US citizen and Canada resident, is currently barred from purchasing a firearm from a U.S. FFL, because in the 4473 paperwork, the purchaser's State of Residence is required. Dearth has no such state of residence and thus cannot truthfully complete the Federal paperwork. The SAF is pursuing the suit on his behalf, stating that the GCA provision, as implemented by current ATF regs, is preventing Mr Dearth from exercising his right to bear arms in violation of the Second Amendment.
The second case is Lane v Holder. Michelle Lane, a resident of the District of Columbia, is unable to take lawful possession of two handguns purchased from an FFL in Virginia, first because of the federal GCA law banning sale of handguns to out-of-state residents, and second because of a mirror Virginia law. To comply with these laws, the Plaintiff had originally arranged to handle the sale through an FFL licensed in D.C., Stephen Dykes, the only FFL in the District of Columbia; however his residential lease, which gave him an address and thus a "place of business" within DC, was revoked so as of right now there are currently no FFLs in DC that could accept the handgun transfer. The SAF is again pursuing this action on Ms. Lane's behalf, stating that the Federal and Virginia laws constitute a ban on the purchase of weapons by DC residents, as currently nobody can do so, and even if Mr. Dykes regains the ability to do business (as DC stated it was working to accomplish as of the motion hearings) the law effectively creates a government-mandated monopoly on the sale of firearms within DC in the hands of Mr. Dykes (who charges $125 per gun to transfer firearms into DC; the going rate most everywhere else I can see for a similar transfer is between $10 and $30 per gun).
If either challenge is finally successful for the Plaintiffs, the Federal law will be struck down for everyone. How many State laws go with it depends on at what level the law is struck down; an appellate court ruling would affect only state laws in the same Circuit but establish the precedent in other Circuits that these laws are violative, while a SCOTUS victory would invalidate any ban on the transfer of non-NFA-registered handguns across State lines. Opinions from the Internet gallery are mixed as to the probability of success of either one; both cases were dismissed by Federal District Court due to "lack of standing"; the Plaintiffs didn't prove they had suffered any "injury" as a result of any action of the Defendants. Dearth was reversed and remanded (Mr Dearth is suffering an "ongoing injury" in the form of being prohibited from exercising his rights as a U.S. citizen under the Second Amendment, almost entirely due to the laws and regulations in place, and thus does indeed have standing), but the case was then again dismissed by the District Court and is again on the docket for the Fourth Circuit. Lane is pending its first go-round in Fourth Circuit, and the case here is weaker; the Plaintiffs admit that if an FFL were doing business in DC, Lane would have no case, while that isn't an option in Dearth's situation. However, they do still have the "ongoing injury" decision from Dearth going for them, because Mr. Dykes is *still* not doing business in DC, despite the reports filed for the hearing over a year ago.