Apart from the massive development overhead the main problem imo is that there will be alot less spots for "higher ups". For example. A RTS/FPS hybrid. the ratio of FPS players to RPG players might be something like 1:100 or worse. What about empire management/RPG/FPS hybrid? 1 king (management player) has many generals (RTS players) who all command many units (FPS players). 1:30:3000? In both examples 99% of all the players will be stuck playing the FPS part anyway whether they want to or not.

One way to improve it might be to market the game as a FPS game and having the fact that its a hybrid be more of a nice extra. Of course that would mean that the game would have to be able to stand as a FPS since 99% of the players wont be the commander and the fact that the commander is another player wont realy add much game value to them seeing as well... They just want to blow stuff up with BFG's... And theyl most likely mute the commanders voice after a while thinking to themselves "WTF i dont want to stand around protecting the crystal mine. Il rather rush the enemy base!".