While Alpha 13 is probably quite a handful as is - especially with SPH having been bumped to it or a later patch - there are a few ideas I'd recommend implementing in it if they aren't already. This list is only for things I think are feasible without SPH, and so it omits broader ideas like tidal heating.
1. Fix multi-stellar system editing.
As it currently stands, attempts to manually edit the behaviour of stars and planets - especially the SMA - in multi-star systems fail. All objects default to, regardless of their location and orbital parent, the 'base' star of the system for their new orbit, and choose seemingly arbitrary values as well. This severely limits the replication of extant multiple-star systems, and can be verified by anyone who wants by loading the Alpha Centauri system, placing a planet around AC-A, and attempting to edit it in the right-click edit panel.
2. Incorporate additional nearby star options.
Fairly self explanatory. At present, only the nearest 100 stars and the nearest+luminous models exist.
3. Measuring tools.
The most useful tool that could be added at present is one that would allow us to determine the distance of a body to another, independent of its orbit. While we -can- do this with some effort at present, it should be a simple thing to code in and was, IIRC, present in the first Universe Sandbox.
4. Brown dwarf heat radiation.
At present, brown dwarves do not radiate heat at all. While brown dwarves are very cold, they do in fact radiate heat, particularly larger brown dwarves.