In the case of the FF set, I think aside from the price, the biggest problem was none of the characters were new and the looks/costumes aren't classic/iconic enough to trigger nostalgia for someone on the fence about a purchase. If that FF set was a classic Kirby FF with classic Surfer and Doom with the new cape, it would probably have been a better seller.
Look at the Marvel Legends Retro 3.75 series, by no means "great" action figures but the presentation/characters/costumes chosen are outstanding.
Marvel Minimates needs to reboot/relaunch the line and get back to basics, focus on iconic looks of characters and avoid the temporary story elements like Elektra Daredevil, Silver Surfer Black. Treat the line like the "Greatest Hits" waves from a few years ago, build out a few waves of ICONIC versions of characters while throwing a bone to the long time collectors by including long-demanded characters and spend a few years trying to build up the customer base.
As far as distribution goes, go back to 2-packs at a higher price point if needed, just make sure the accessories included help justify the pricing. Make these 2-packs the core of the Marvel series featuring the big names in bright iconic costumes (ala Greatest Hits). Supplement these 2-packs with boxsets (maybe DST Direct timed pre-order exclusives) catering more to unique looks, modern or alternate costumes, and lesser known characters for the long time collectors.
Marvel Minimates needs a new #1, but keep the legacy numbering.