* Is the whole conflict with Abstergo and Vidic still trying to hunt Desmond and company down get resolved properly?- Oh, yes it does, I can say that. And, without being too specific, let's just say Vidic FINALLY gets what's coming to him. BIG TIME. And it's SO satisfying when it happens. Also, before that confrontation, we do get to see Desmond come face to face with Daniel Cross from "The Fall" and "The Chain" comics and the multiplayer storyline.
* Speaking of Desmond, does he get some action this time and not just stay in the Animus the whole time?- Yep, there's a couple of missions with him that take place outside the main hub area in the Vault where everyone's set up shop with the Animus. The aforementioned resolution to the Abstergo/Vidic storyline takes center-stage in the last of these missions towards the end of the game. These also take place between certain Sequences in the Animus, namely right after Sequences 5, 8, and 10. Don't worry, they still look fun, though!
* Are there any more Subject 16-related stuff/hidden mini-games related to the present-day plotline in this game?- Not that I know of, though I'm not entirely sure. While there seems to be plenty of side-quests in the game, the video walkthrough series I saw didn't seem to hint at any similar hidden side-quests like the ones from AC 2, Brotherhood, and Revelations to be found this time around. I'll know more later this week after I pick up the game.
* Are we given more info on Juno and Minerva this time around?- Yes, and let's just say there's more to what happened to them than has been let on previously....
* What's the deal with the guy you play as early on, and who exactly is he?- The guy you start the main Animus sequences storyline as is actually Haythan Kenway (and, no, that's not a typo: that's actually how his first name is spelt), Connor's British father. I won't spoil it, but there's a MAJOR plot twist regarding him that's revealed at the end of Sequence 3 (the last time you play as him) that's gonna make ALL OF YOU scream "WTF?!?" in shock! Hell, when I first saw it happen, I certainly didn't see it coming and I, too found myself blurting out lout in surprise! It's a brilliantly crafter twist, and it sets up the conflict for the rest of the game in a way that's radically different than both Ezio and Altair's storylines before this.