Toyota said the issue does "involve the variable valve timing," but both Subaru and Toyota say the issue is entirely about the software, that the ECU can develop a "handshake issue" with the engine after having an unfavorable "reaction to normal mechanical variations" in a small number of cases.
The two automakers diverge on the remedy, however. After 100 miles of learning the powertrain and the driver's driving style, AN reports that the ECU's mapping is pretty much baked in. If engine operation exceeds the established parameters, at low revs the engine succumbs to uneven idling and stalling as the ECU tries to recalibrate to a new range of tolerances. Toyota has said that if the issue is suffered by a car with less than 100 miles, the ECU should be reflashed, but that cars with more than 100 miles should have their ECUs replaced. Subaru, though, has said that the ECU doesn't need to be replaced no matter the mileage – a reflash is all that's required. It appears that some owners who have had the reflash have suffered the problem again.
We don't have any hard numbers on how many of the coupes are afflicted and how many have been fixed, so it's impossible to know how big or little the issue is. But with the popularity of the twins and the vociferousness of the fans who queued up to buy them, the situation will either be adequately resolved or we'll be hearing a lot more about it soon enough.