I like this idea... more replayability...
Think about it, werent you sick of starting on Peragus all the time... why not have two starting points this time eh?... never seen that before (i think...)
To be on topic... I really think that the main char will be connected to the Handmaiden somehow (like someone jus said)... Whoever he/she is, i hope that its not obvious like the son/daughter of Bastila+Revan or Carth+Revan...