Couple of issues with multiple servers.
1. People will in-large, always flock to the higher populated server.
2. CM is refined for a large player-base (100ish min)
Concern I believe in-term of gameplay is the second server not maintaining a minimum of 100players in order to stabilize it effectively. Since the game has moved to a TDM, this would make balancing the game out almost impossible as you'd have two different servers experiencing balance issues primarily due to player count making it near impossible to balance correctly.
Additionally you'd run into a lot of "Server Hopping", where a marine player would leave the server and jump to the next one to continue playing as a Marine. This would once again, affect balance in terms of aliens as they'd lose players who will just fuck off for a "Fresh round".
Basically a lot of balance problems and thats not even getting into the tech issues.