The 3x3' has an extra square foot, is an extra foot deep, and is square, so you'll get more even light distribution.
Take it from someone who uses two 2x4x5' tents. I bought them as my first tents I owned eight years ago, and only reason I went 2x4 as opposed to 3x3 was I was limited in the closet I had them in for width. If I went 3x3, I would have only had one foot of space to operate in front of them. (I now use them both for veg only, and flower in two 4x4').
Given the space, I'd go 3x3' over a 2x4' every time.