Also, I'd say that the difference in accelleration between not having the flaps down for the first half of your takeoff run and having them down would be relatively insignificant, as drag increases with the square of the speed and is therefore going to be on the low side at low speeds.
I have heard of people doing what you said, i.e. putting the flaps down partway through the roll, timed so that they get to the desired takeoff setting as rotate speed is reached, but I couldn't see it making too much difference, especially considering that the real drag penalty of flaps doesn't really manifest itself until you get to the high angle settings used for landing.
Additionally, the chance of forgetting to put them down at all is increased if you don't do it and check it during the pre takeoff checks.
[ 14 August 2001: Message edited by: Arm out the window ]