Customizable characters made from parts won't happen, at least not in a long time. In fact the time is so long I'm not going to have it in my mental todo-list even

Map-specific and team-specific collection of soldier models will happen, so there will be more variety in that aspect. I'm sure we'll start it as a random thing, but it could evolve to support player preferences as well. One possibility is to bind weapons to outfits, but it's not decided yet.
About seeing other people's squads, I feel something more subtle would be needed than spamming the leader colored markers for the mates at all times -- after all, I don't see such a huge need for this feature to justify marker spamming

Maybe the squadmate markers could be shown if you take the crosshair over a leader, as in inspecting the soldier's status. Inspecting a squadmate would show the leader with a marker then, perhaps.
There has been some discussion about flags, probably in IRC, to further indicate base capture areas. Agreed, the flags wouldn't happen in the middle of battle zone in real life, they can be quite the welcome for the enemy. As you anyway can't hide your base from the enemy in RWR, I think the flags could be used but only at the very heart of bases. They help to indicate ownership and thus importance of spots to defend / attack to, and waving animations are lively. The bases do not need to be filled with flags, one per base could do it. A flag pole works fine without buildings too.
The flags aren't seen a huge priority at the moment either, dedicated servers (80% done!), AI driving, map 4, revamped item system, content packages, soldier models, stuff like that will still keep me busy for quite a while before I can get to add eye-candy / usability improvements.