#2) Don't award energy or skill points for it. Make it something you get a fun rewards currency for. Maybe based purely on time spent active in the Holodeck or simply a once a day award for running a mission that meets certain criteria.
#3) If you DO award meaningful stuff for Holodeck missions, have a check system in place. Ie. It only awards stuff for a mission complete and only allows one hand in per half hour, similar to the repeatable cluster exploration quests from Sulu.
No, this is crucial. This will make or break STO with many players.
The biggest single problem STO has is lack of content. Player created content is what? Say it with me, content.
I've been proposing a two stage system for player created content to cut down on the nonsense we saw with architect.
Stage 1: The Holodeck
This is basically just like Architect from CoH with the added advantages of the Genesis toolkit and other indoor settings. However no rewards will be given out for the creating or playing of any Holodeck mission. This is just for fun. Players can use it to make adventures for friends or to create backdrops for events and so on (much like Storyteller in SWG). But nobody will get loot, rewards, drops or even so much as a pat on the head. The main reward will be that folks enjoy what you can create and beg for more. That's a huge ego boost for those of you who haven't tried it yet.
Stage 2: Subspace Transmissions
A player creating a Holodeck mission can apply for it to be considered as a Subspace Transmission mission. These will be developer screened and approved Holodeck missions designed specifically as Exploration missions. Each will have a text intro that's some emergency communication to a vessel's commander and they'll have the option of warping directly into the mission when doing Explorations. At this stage both the designer of the mission and the players do get rewards. The designer gets credits for the C-Store and players get the usual drops and experience gained for a mission (along with a point toward the completion of an Exploration mission series).
What this should do is cause fewer crap missions to come about and the quality of overall player generated content to be much higher. And higher still for those wanting those C-bucks. In time Exploration could be full of an infinite variety of missions hand-crafted by players in addition to Cryptic Genesis missions and missions from other sources (NASA for space exploration missions, etc.)
I love the Stage 1 aspect they could add some sort of Holodeck grid to any of the space stations and you can if bored enough grab a few friends or even auto group and play some player created stories. Keep it for fun only no "real" rewards like you said and no skill points just for the goofing off aspect would make it great. Now you could add a specific set of things you can "win" inside of the holodeck you could unlock better holographic weapons or get other items to boots your performance just inside of the holodeck make it something to do for fun outside of the main game.