Modflow has a lot of packages that allow it to simulate boundaries and other processes not present in the base code. For instance, MT3DMS and SeaWat allow modeling of solute and energy fluxes and variable density flow.
Sutra does not have modular packages that add on, but it can consider solute and energy (which it treats as a solute) flux and variable density flow natively without additional packages. I think that in order to add boundaries not included in the base model, rather than turning on a package, the Sutra code must be modified and recompiled.
Modflow requires less computational power than Sutra (generally), but because it is a finite difference grid, rather than a finite element mesh, you cannot refine cells around areas of interest as easily.
There are many GUIs that can be used to pre-and-post-process model inputs and outputs for both modeling packages. Some are better than others and the prices vary considerably. Model Muse is freeware from the USGS. The GUI works with both Modflow and Sutra, so it may be a good place for you to play with both modeling packages to see which one better fits your needs.
Good luck.