It seems to me that a system like the Klingons in ST:O makes some sense (not that I know a lot about it). Players with sufficient XP could create an alternate pilot that is part of the clans with beginner stats/no modules. This idea has three things going for it. One, clan players will be better warriors on average than other players, much like they are in the canon. Two, this will probably stem the feared flood of players from the IS to the Clans since only experienced players can do it. Third, this will motivate people to play more so that they can be eligible to play a clan pilot.
My other big thought comes from the fact that in the novels the clans bid decreasing numbers of pilots to accomplish objectives with greater prestige going to sending fewer mechs into battle. This could be implemented by having greater rewards go to clan players in a match who send fewer than maximum numbers of players into the battle. For example if in 12v12 battle the clan players only send in 10 mechs then they get double XP for the battle (not saying that is the real/best rate, just an example). Alternately clan "corps" could bid to fight battles, bidding progressively fewer and fewer mechs. Either system might counter the reality that ton for ton clan mechs are more deadly than IS mechs by encouraging the clans to fight with fewer mechs.
Just some thoughts
