It's the same reason ILM built an off-the-shelf AMT Enterprise model for the movies - the 6-footer just doesn't look right when scaled down.
Unfortunately, the effects team got tired of the 6-footer, so they used the 2-footer inappropriately during season 2. I don't think the janky-looking deflector was ever meant to be shown close-up. Between the 2 and 4, using the 4 going forward was the lesser of two evils. Thank goodness the 6-footer got to be used one last time in Generations (not counting BOBW).
BTW, if you are curious, the AMT Refit Enterprise was used in these shots:
And here it is at auction: http://www.mutara.net/Christies/MiniEntA.html
I notice in The Schizoid Man in HD, the ship warps away from Graves' World still using the 6-foot model. The scaling gets pretty bad when it zooms away. Odd choice.
Also interesting that the 2-footer disappeared without a trace. I wonder if it will ever turn up. I saw the 4-foot model up close at a Star Trek exhibit. It looks awful. It still has scars from the All Good Things modifications.