You lose the following:

1) Guild Marks (Job Abilities... chances are more will be added, so if you have like 2000 and some new say Advanced job ability cost 30000 marks or something... yea you will be screwing yourself for awhile)
2) Faction Credit (Several of the best pieces in the game for certain jobs drop off those, and chances are this system will be expanded on later, which could cause issues later on if you have no credits)
3) Bonuses to Gil and Mark for doing leves in multiple regions (1 star bonus vs 2)

You gain:
1) Much higher sp/hr
2) More monatany.... seriously doing the same 6-8 leves every reset every month is boring as all get out