I think we would be able to implement a stat bonus for fighter squadrons (squads) that work well together in the form of teamwork points. For instance, if a member of your squadron damaged an enemy fighter and you finish him off, you would get the kill, but your squad mate would get a kill assist. Things like that would probably work well.
I like your ideas Talon, but I think an approach that offers a bit more freedom would be more in the BF spirit. I like your idea about giving squads their own hangars, however due to limitations of both star wars lore (most ships only have 1 or 2 hangars) and geometry induced lag (more hangars = more lag), we will probably only have a max of 2 hangars on the largest cap ships (realisticaly, more like 1).
Spawning vehicles 6 at a time is a recipe for disaster, that many polygons and detailed textures all at once in a very small space would also create lag. For that reason, ships will probably spawn in groups of two (this is highly unofficial, just an educated guess), and after the first two have been taken, another pair will spawn a little while later. While this may make it harder for squads to stay together, it is necessary to reduce lag and increase hangar space.
The best part of your ideas come from squad specific spawning. Using squad specific spawn points, you allow squads to spawn closer to the tools they need, while making others spawn in different areas making it harder for loners to steal fighters and transports to go off on their own with.
I think the best way to do it would be to make it such that the fighter squads spawn in their fighters optimally. We could make it so they have access to all of the common spawn points in case there aren't any fighters currently available, but say when an X-Wing re-spawns in a Hangar, members of the X-Wing Squadron can spawn directly into it. This would facilitate the fighter squadron members, but wouldn't necessarily restrict other players.