Both the 1000 and the 2000 have their benefits and flaws, it depends on personal preference at this point really.
The 1000 has the OLED screen and (to me anyways) is a lot more comfortable to hold.
The 2000 has an embedded 1GB of storage (which is useless if you get a memory card, it gets deactivated once a memory card is inserted), a Micro USB port instead of the proprietary Vita one, and various cosmetic changes (different color versions, smaller rear-touchpad, changes in the Start/Select button).
I would recommend actually holding both the 1000 and the 2000 before you decide.