Just feel like ruining the storyline for you guys by pointing out a couple massive gaps in the plot I noticed.
Just kidding, they're just minor plot holes I noticed.
SPOILERS BEGIN NOW.
In the Future chapters, if you have the top screen set to Map and Team in the Options section, you can clearly see that the events in the Future take place in the Hidden Land, yet when you, your partner, and Grovyle return to the past, Grovyle states he doesn't know where the hidden land is. Perhaps he means he doesn't know how to get from the mainland to the hidden land, but then how did he get to the mainland to identify locations where Time Gears were hidden?
Lapras states that it is impossible to enter the hidden land without the relic fragment and pure intentions, but Darkrai managed to get in to sabotage Temporal Tower.
Wigglytuff's Guild is clearly a coverup for a drug processing plant. Croagunk is either a serial killer (in which case he uses the cauldron full of sulphuric acid in the back of his "shop" to dispose of his victim's bodies, and then trades off their possessions to you and your partner), or a drug manufacturer, in which case his cauldron is really a meth lab, and the items he trades you are probably attempts to plant drugs on you and your partner in order to get you arrested. Chatot is that bipolar, angry, calculative guy that is necessary to every illegal operation, Chimecho and Sunflora are to put a happy, innocent face on the operation for authorities, Loudred and Diglett's supposed "senty" duty is really a look-out system for the cops, Bidoof is a hillbilly drug runner, and Wigglytuff is obviously a robot, or maybe a hitman in disguise.
I'm so getting infracted for that last part...