It all depends on whether they think they'll make more money releasing one third version, or two sequels.
I have a feeling two sequels may be the norm from now on. They probably make more money with the sequel thing. Those ds/3ds cards can't be that expensive to make, and a sequel catches all the people who buy both versions.
http://www.youtube.com/watch?v=GtxCr5ju2EE&feature=related - If you played Mystical Ninja 64, you need to click this.