Well, here are some questions to ask yourself:
1) Which would you rather make?
2) Which would you do a better job of making? (I feel an RTS would be far more difficult to make, but might suit you if you're more strategy minded than musical)
3) Which would you rather play yourself?
4) Who do you want playing your games? A good rhythm game could get you more casual fans, a good RTS could get you more technical fans.
But. yeah, as No Time To Play says, the answer depends very much on you :)