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The current recommendation is to use Kinetic. See also wiki/Distributions.
There will still be a difference in the nr of packages supported by both Indigo and Kinetic, but that is something that is true of all ROS distributions (ie: Hydro and Indigo showed a similar difference).
And as @jayess hints at: if you need something that is not available on Kinetic, chances are high that building from source in a Catkin workspace -- which you will need to create for your own work anyway -- will work, as the differences between Kinetic and Indigo are relatively minor for a lot of things. The wiki/kinetic/Migration page has info on that.
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