The problem with it is its not that easy or convenient when a group you actually want to run pops up. You saying "alignment can be changed instantly in the pocket D, and TUNNEL/bases allow you to teleport anywhere from anywhere" is completely disingenuous, because it takes minutes to do these things. Most people don't want to ask 7 other people to wait as they:
>leave the mission
>walk to a portal
>teleport to blue side
All to just to be able to accept to the invite. Sure this isn't a ton of work, but it takes awhile. Awhile for absolutely no reason whatsoever I might add. The reason Red side is so empty all the time is 95% of the player base doesn't level on red side. A huge reason that being invited to a group just takes awhile. This is what I mean by convivence.
A lot of people not liking the content is probably true. However, I think a lot of people realize that choosing to play red is basically choosing to be completely unable to interact with the majority of players.