One can increase the capacitance with a change in the dialectric. A trench cell is good for smaller packaging. A trench cell is also susceptible to noise from the substrate. Logic consumes a lot of power and injects noise into the substrate, and this could be bad for trenched cells. The stacked cells can be affected by noise in the upper layers.
Stacks are more popular and are easy to make small.
Stacks are easier for Samsung to build than the trench. The stack lends itself well to mass production. The new 1 GB chip from Samsung is 652 mm2. Many DRAMs operate at 5 V off chip, and at 3.3 V for internal chip operation. The 1 GB DRAM from Samsung used 1.8 V for the memory array.