The Bioware blog recently posted about this information, which I'll summarize here.
Mechanics
Earning reputation in Mass Effect 3 is a bit different from the first two games. Rather than earning only Paragon and Renegade points, you can also earn Neutral reputation, so there are 3 types of rep in ME3.
This means you can now mix being Paragon/Renegade without worrying about getting locked out of the more difficult Charm/Intimidate options. When you earn Paragon/Renegade rep, it'll show up as Blue/Red, whereas if you earn Neutral rep, it'll increase your reputation bar's size as a whole while retaining the same blue/red ratio.
Click through for the larger version.
Your total reputation (blue/red/neutral) will determine whether or not you'll be able to pass a Charm/Intimidate block. The lines on the bar are "checkpoints" which serve as gates for more difficult dialogue options. I marked them with the thin lines of red, in case it was difficult to see (this is not my Shep, this is the photo from the blog post).
As per usual, you get rep from completing missions and making dialogue choices. For missions with no Paragon/Renegade choice but still have a large impact, you will get Neutral rep.
Story Impact
In contrast to older Bioware games, you can never actually be the villain in ME3, though this should be rather clear from how they handled the first 2 games. No matter what, you will be fighting to save the galaxy. The manner in which you do it will be what differentiates a Paragon from a Renegade. Also, bullying people into giving you more money or discounts won't be the crux of what makes a Renegade decision in this game. Who needs credits if there's nowhere to spend them because civilized life has been destroyed?
Reputation gain will be based on when you have to make a decision in the game. Here are a few examples of what kind of rep you would get, taken from the blog:
- Confronted on the Citadel by a desperate refugee with a gun, you give her some credits and help her find a place to sleep. (Paragon)
- As a human colony falls to Reaper forces, you order down an orbital strike, brutally killing thousands of colonists to prevent the Reapers from turning them into husks. (Renegade)
- You land at a turian fuel depot taken by Reaper forces and clear it out, enabling allied forces to keep fighting. (General Reputation)
TL;DR
BioWare has finally made a single-player game that lets you make morally grey choices without nerfing yourself, gameplay-wise. Rejoice!
Javik the Prothean is a DLC only squad member that's available in the "From Ashes" DLC:
Access to From Ashes is included free with all copies of the Mass Effect 3 N7 Collector's Edition and the Digital Deluxe Edition. It is available for purchase separately for 800 Microsoft Points, 800 BioWare Points, or $9.99 USD on PlayStation Network.
And as @LessPop mentioned, the events in previous Mass Effect games will mean that there will be some squad members that are completely unavailable in the game:
Ashley/Kaidan depending on choices in ME1, and Garrus and Tali depending on their survival of the suicide mission in ME2.
Other than that, the only way to 'miss' a squad member is to follow certain decisions in ME3 which results in their death. There's no way to avoid recruiting any of the non-DLC squad members in ME3, they all show up as a part of the main quest.
Best Answer
No, missed items will be available in shops. If you've missed more than one item of a particular type, the next item will only be unlocked after you bought the previous one, not necessarily in the same shop. You can check the available items in the shuttle bay.