Two big reasons for me why I always prefer to do inclines before flats are that I feel they are safer (when's the last time you heard of someone tearing a pec while doing inclines?) and because I feel it's better to concentrate on upper pec development due to the lower pecs always getting involved no matter what chest movement you do.
Also, since I normally train alone and therefore do more dumbell work than barbell, it's a lot easier for me at the conclusion of a set of incline dumbell presses to get the weights back to my thighs and then to the ground than with flats. With dumbell presses on the flat bench at the conclusion of the set taken to failure, I can't get the bells back up to the top in order to easily rock back to the starting, seated position to easily place the weights back to the floor. Instead, I have to either drop the weights to the floor like Ronnie Coleman and cause a scene with the noise (not cool, but sometimes necessary) or try to rock back up with the weights still near my shoulders which is pretty dangerous if you're using a substantial amount of weight. By doing inclines first and doing flats later in the workout, I end up using dumbells a bit lighter than I would had I started out with flats, and therefore they're easier to dispose of at the conclusion of each set of dumbell flats. For me, I use either 125's or 130's, so doing the rock back without being able to get the dumbells up to the top first is a bit dangerous and could easily ruin my shoulder joints. But it's still better than using 140's which I would be using if I had started off with flats in the beginning of my workout.
