To be honest, go with the one you feel more comfortable working with or the one you have more experience with. That way you can make the game in the limited timeframe, since you can plan better how you allocate your time in that particular game workflow.
Also, keep in mind that in 2d there's usually a bunch of sprites that require to be made/edited, most likely in a time consuming hand-painted way, while in 3d you can make/edit a pretty decent model with a few clicks in Blender. Once again, it depends on the skillset you have as a developer.