I am (maybe) going to play JediAcademy through again but...
can I somehow add new model with different piece/skin/color
options to the game ??

Yep, it's not difficult to do. Heck, I did it with zero skinning experience. All you have to do is create the nessisary additional skin files and a playermodel.txt. You can find good examples on how to by just checking out the model directories for the jaden models.

*shameless plug*
OR, you could wait until I finish my already WIP CoOp gametype for JKA.