I don't have a dog in this fight since this doubles tournament is falling on a date i have to be at a wedding.
I did a few 1250/2500pt doubles tournaments in 5th and i hear what people are saying about not making it past round 3. 2500 points of stuff on the board makes for a long game on its own without adding the component of having to discuss strategy with your teammate (i'll shoot the Daemon Prince in the face and you get to the objective, no no no YOU take the objective and I'll shoot stuff in the face )
On the other side of that coin a 1000pt limit makes for a difficult army list for several codexs who only have expensive options to choose from and probably few will bring expensive HQ choices (which may not be a bad thing). It's going to lead to less than competitive lists for some but i guess that is where your partner comes in to fill in the holes in your army.
Whatever is decided (1000 or 1250) perhaps Chase could add a box to the score sheet and have everyone fill in what round they made it to after each round? It would be a great tool for BG to gauge what point value to do the NEXT doubles tournament at in 2013