Speaking of Mario and Luigi Partners in Time, the whole time travel thing...well... wasn't really important (to the story?) at all. The only thing you used time travel for, is to get to new areas, and to gets the baby forms of Mario and Luigi. You may have noticed that the only place you can ever visit in the present is Peach's Castle.
Also, the time paradoxes hardly seemed to fit. (I think there was only one anyway.) When you douse the Thowmp in Elvin Gadd's House, his future self instantly gets the smarts to make the hydrogush 4 thousand-whatever-number. On the other hand, the shroobs have the castle in the past, yet they do not have it already in the future. In fact, the future does not seem to be affected at ALL by the shroobs, except for the time holes. Seems a little inconsistent.