According to this news on IncGamers, Cryptic wants to let us explore our own ships. Makes sense, we could have quests in the Holodeck and with crew members. I'd love to be able to actually see the inside of my ship and, ya know, actually meet some of my crew :P
http://www.incgamers.com/News/21011/cryptic-wants-to-open-up-star-trek-online-ships
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Actually, the 45 day patch is a small patch, at least according to a dev interview. A large content patch is like the new free expansion that's coming for Cryptic's other game, Champions Online. Which if you notice is coming out at about 7 months after release. I'm only going on a remark a dev made saying 4 months. It's quite possible the first large content patch for STO will be closer to 7 as well.