One sollution would be a reduced fee for Klingon players to reflect their reduced content. As Klingon content improves (relative to Federation and other factions) the fee goes up. That gives Cryptic a finfancial incentive to improve Klingon content (content = PvE + PvP + customization).
I rate the "worth" of a Klingon only subscrition to be no more than $5/month in comparison to a $15/month Fed subscription. In reality ********* charges $5/month but delivers far more content than a STO Federation player gets (except for the picture quality).
I suppose this could work. Let the player opt out of ever making a character of a different faction and reduce their fee. You couldn't simply tie it the level of klingon content though. You would need to ensure that the people choosing this option would never get access to the full game.