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.
Personally I would like to see them take all the featured foundry missions and just add a Dilithium reward to those (say 300 Li2), have a timer so you can play the mission only once per day (or only earn the reward once per day) and limit the reward to three missions per character per day. Every week they would add another featured mission or two to the list.
My Romulan Liberated Borg character made it to Level 30 and beat the (old) Defense of New Romulus with the skill point bug.
I'd rather not see another form of currancy that can only be used in a certain shop that carries nothing worthwhile.
YES, by all means do create rewards for the missions that people have spent so much time crafting. Right now the responsibility for rewarding this hard work falls on those who partake in the missions (tips), thus creating a loss for the participants involved.
There are guidelines that the official STO team uses when building area as to how much they put into it, apply those guidelines to these missions as well.
OR perhaps setup a system where you add in 30 squares of floor space, and 50 objects, it entitles you to place a scannable resource. Place in 20 level appropriate adversaries and you can toss in a dropped weapon/item.
Three space battle opponents, a ten room ground mission, followed by 3 more space battles, and you can rescue a random duty officer. (Can be done once every three days)