I'm sure a new model format has already been suggested or maybe there's even a ticket but here I'm recommending the MD5 format. It's probably the most compatible format that supports skeltons and separate animation files (md5mesh for meshes, uv and skeleton with weights and md5anim for skeletal animation that can be used by any md5mesh with a matching skeleton). This is the format I use to convert my 3ds max models with skeletal animation across into blender where I export into the g3d format.
Here's more info on it: http://www.modwiki.net/wiki/MD5_(file_format)
I also noticed that GlestNG is looking into it so if that engine gets big, it means more compatibility.
I'm not sure about the licensing for it, I don't think there is any as it's more to do with the models and tools than the file format which is plain text it seems. It's a much lighter format and with md5anim multiple models can share the same animations saving a lot of file space and development time for modders.
With skeletal animation we can set bones that are used as a reference so when firing projectile attacks rather then setting the offset in an xml, you can refer to a bone as an offset instead. Also moving turrets and maybe merging animations could be used (one md5anim could have a walk cycle that could then have say the upper body bones of the model taken over by something like an attacking animation so a unit can move and attack at the same time without having to make a separate animation for it).
For now though simply replacing a g3d model with an md5mesh and md5anim anims would do, future features could be implemented after. To use this in the xml, the md5mesh should be defined at the top which would then make GAE know that this unit uses md5 instead of g3d, then md5anims should be referenced to for each skill in place of where separate g3d models were.
Anyway there's a nice huge wall of text, using md5 instead of g3d means I don't have worry about any g3d limits as I have too many g3ds for two of my factions to run in the same game at the minute and reducing their aniamtion frames any more will ruins them.