Simple enough: People have been asking for more content in-ship, and I've seen multiple "Ask Cryptic" installments in which Holodeck functionality was requested.
The current direction seems to be to make mission replay something one can access directly from a Holodeck (SFA or in-ship). I would personally prefer that this be expanded to include Foundry mission access.
Take the Foundry mission from your ship interior's Holodeck (or in one of the Holodecks at SFA or KDFA), with any team-mates you might wish to join you invited to your ship's interior and standing in the holodeck with you, then map move as a group to the mission's first map. At mission's end, return to the Holodeck on board that same ship's interior.
It would be a far better use of and explanation for the kinds of missions we are seeing, right down to a immersive reasoning behind each mission - it is a Holodeck program from another captain you can chose to experience.
I'd even prefer we be making missions there as well, but clearly there are reasons for the clunky system we have now where a new character for creation-only is required... or else why do that?
Afterthought: If Foundry Missions become officially Holodeck simulations, there would no longer be any licensing problems promoting some to "official" missions, as the primary roadblock I can see is the fact that any UGC made into an "official" mission would become STO Canon. This is avoided completely by merely suggesting these are Canon examples of Holodeck programs, and not actual Canon events in the STO/ST universe.
My mission I want actually in the game world as part of canon, because it ties in with game canon - it was written that way. I agree that they should add Foundry mission access to holodecks, but only for missions labelled as being holodeck missions or replay scenarios.
You can now hook up Foundry missions to start from one of the holodecks on Starfleet Academy (by talking to the Ferengi guy in one of them), so if an author wants to make a holodeck mission, they can choose to start it from one.
I've been against this idea when Paragon Studios created their Architect Entertainment (the UGC environment/toolset for City of Heroes/Villains) and I'm definitely against this idea for Star Trek Online. I'm not going to claim that the missions I — or anyone else for that matter — write actually "happened" as a part of the STAR TREK universe as portrayed by Star Trek Online and I think this choice, whether a Foundry mission is nothing but a Holodeck novel or something that "happened" to the players playing it, should be offered to both the author and the player.
I don't like the idea either. Obviously Foundry stories are "unofficial". However, you can write a lot of stories that don't step on any toes in the "official" universe, and thus can be considered to legitimately exist themselves.