The Mario and Luigi series of portable Mario RPGs has only gotten better with each entry, beginning with Superstar Saga and continuing in Partners in Time. Take the excellent writing and RPG formula of the series and add time travel, and the results can't be anything but awesome. Playing as Mario and Luigi and their baby counterparts in Mushroom Kingdom's past was an interesting choice, but it worked well. They even threw in some aliens called "Shroobs."
Mario and Luigi: Partners in Time (2005)