I personally won't get hopes up but I'm hoping it's smaller or less instanced.
I really hope for the day when they provide territory that can be fought over, until then the sector space on the map is just annoying or boring to fly through. I wouldn't mind getting sucked into an enemy contact if KDF players were getting sucked into the same instance to fight me. Now that would improve all sector spaces and make it truly worrying to get a random engagement with the enemy
The secret project for S3 is more than likely User Generated Content.
They've hinted at us being able to add missions to the existing universe. Which would make it better than City of Heroes Mission Architect where everyone must go to the same building to run UGC missions.
5. More "Iconic" missions - The other night my girlfriend and I took on the "Guardian of Never" episode. She absolutely loved that mission! For me, this is one of the best missions I have played in STO. More content like this would be nice. Perhaps not always a time travel mission, but missions that provide interaction with iconic people, iconic ships and iconic places.
8. Restore the Khitomer Accords. (Not very likely, but working together with the Klingons would likely make the Klingon players much more happy than the currently broken and dying PvP system.) Factions don't have to mean Us vs Them. Cooperative factions where the Klingons and Federation are allies once more, and do things together, but mostly focus on their own issues in the Empire and UFP could very well work.
9. Meaningful PvP that isn't broken, and based on Number 8, doesn't depend on Faction vs Faction solely.
I got the impression from some of Dan's comments that Season 3 is going to have a strong focus on polishing the game's existing components. I definitely could see UCG being the big "secret" and a good way to justify less "new" content. I'm sure there is going to be some new stuff, but I completely support less new things at the cost of making what is currently in place function to it's max potential.
I know he's mentioned a couple times that Memory Alpha and Exploration missions are high priority items on his list along with sector space improvements. It's also safe to assume Klingons will get something along the line of a few more specific missions to help balance out content between the factions. I'm curious about the weekly episodes though. I got the impression the first 5 or so are already done, but they're taking a "let's see how this works" stance before committing to more. One could assume that Season 3 is also going to bring more weekly episodes if they are a hit or other faction neutral content depending on how the episodes go over.
For the details the Dev tracker located here http://forums.startrekonline.com/forumdisplay.php?f=64 is an excellent resource to know exactly what the dev's are saying. Dan has been EXTREMELY communicative in the last week, so just searching for his posts would shed a lot of light on his thoughts beyond Season 2.