What exctly do I have to add here?
Given a game for 2-6 players with 2-6 different factions/colors, do I have to add the 6 colors or the possible setups?
For example, the Pax Romana module uses more player sides as there are factions in play. They have some for two player games and some for four player games. I don’t know exactly for what purpose.
In case this is important for the answer, the game has the possibility of player elimination and the player who eliminates another player gets ownage of his counters.
Wow, I don’t thought this is such a hard to answer question. 
The lack of replies so far might be because your question is actually not so easy to reply to. Whereas other aspects of Vassal are very advanced and sophisticated, the all sides implementation is probably just a bit spartan and uncustomizable.
In my understanding you cannot really have pieces - with a restricted access trait - switch sides at all. Those sides are fixed and not dynamically changeable (would be a nice feature in the future).
If I understand your problem correctly you will probably have to define the 6 sides for your 6 potential players. Then you will have to forget using restricted access traits to enforce ownership of pieces and, instead, use restrict commands on the piece prototypes.
The restrict commands should check global properties you will have to define dynamically along the way (at game start and/or whenever some piece swaps ownership, due to elimination), like who is supposed to be in control of this piece/card and if he/she is the current player in the given game turn and can thus manipulate this piece or not etc.
In other words: your friend is “restrict command”, not “restricted access”, I think. ![;)]( "Wink")
It’s not the best possible friend, though… Not only because forces you to code lots of global properties, checks etc. But also because this way you can only block commands and not accidental/malicious movement of pieces by unauthorized players. Either you trust them not to move others’ pieces or you set move piece to “never”. Then you have to add potentially lots of send-to-location traits (for which restrict command works) to take care of movement by right click commands, triggers, whatever. Unrealistic if your game is the typical miniature wargame with hexes and such. More realistic if it’s card based with few units around, maybe.
I feared it would be that complicated. Thanks for your answer anyway, I think it will help, at least deciding if making a module for this game is worthwile. 
It’s an area-based game where you move stacks of counters. It is crucial that other players don’t know the content of stacks, but often players will have to reveal parts of the stacks.