I have found that Foundry missions show a great deal of creativity and adds a huge value to my STO experience but the main problem people have with foundry missions is that fact that there aren't any rewards (other than Investigate Officer Reports Daily rewards).
My suggestion is to create a store using an additional currency, yes I know, ANOTHER currency. This store would have special items, anything from items like you see in the lobi store to mk xi and mk xii weapons, armor and ship items and perhaps some specialty items like Romulan or Cardassian outfits. The currency would be rewarded by doing Foundry missions, thus providing an incentive to play these player created missions. There is an obvious issue with this plan which would have to be resolved, which is the one click missions and the very short missions you see in the Community Authored section. This would probably require some kind of approval process to weed out those missions. Hopefully the issue of having another currency would be less of a problem since we are seeing a reduction in currencies in Season 7.