I think Dave covered most of it. Just to add a bit, the 3000 has many more software features as well (multiple jumps, back/forward jump...)

It is lighter and uses smaller batteries (AAA instead of AA) so it is normal that it would not last as long. I agree with Dave about the charger, but then again I have always had Prontos with chargers and would never think of getting one without it (be it 1000,2000,3000,6000,7000) the convenience of the charger (remote always ready, because you know batteries always run out at the worst moment) is incredible and in most cases there is the added benefit of making the remote easier to find.

also the 2000 was out of production over a year ago and the 1000 more then 3 years ago.