This is my theory connecting Gen 1 to Gen 2:
Makuta Terridax survived the battle for Bara Mangna, even though he was killed by Mata Nui. How, you might ask? Well, remember that Terridax is an energy cloud, which is how he got control of the Mata Nui robot in the first place. When the Moon hit the Mata Nui robot it the head, the moon killed the robot body, NOT Terridax himself (energy can never be created nor destroyed). Of course Terridax probably took a while composing himself after his "death." Eventually, I believe, he would rise/reawaken again and fly off into space (he is energy after all) looking for more power. All the Toa, Glatorian, Matoran, Agori, and Turaga notice Terridax's reawakening. They decide on launching toa canisters (with the Toa Nuva inside) into space to follow Terridax, while the rest of them would stay and try to build a rocket to go after Terridax (or something like that). Meanwhile Terridax (being energy, is faster than the Toa canisters) flies over to Okoto and sees the Okoto Makuta's jealousy for his brother Ekimu. When Makuta builds and puts on the Mask of Ultimate Power (thinking it will give him enough power to stop all threats and have the villagers praise him instead of Ekimu), Terridax (being energy) flies into the mask at the last moment, and takes control/ corrupts Makuta. When Ekimu knocks the mask of Ultimate Power off of Makuta's face, its too late, Terridax has already corrupted Makuta and now is in control off him and his actions. Terridax/Makuta now wants more power in order to destroy the Gen 1 Mata Nui, Toa, Glatoran, etc.
"Wow" some might say. That's pretty in depth stuff, but you forgot about the Toa Nuva in the canisters flying through space, and what of the mask of Time?
To that I continue my theory...
So the Toa Nuva are traveling through space when they smash into the planets that are seen on the prophecy wall in "The Legend" video on Lego.com. From there they are unconscious. At this point enough time has passed as to where the protector villagers use the upper half of the mask of Time to summon the Toa. In reality, the light shot out of the Mask (as seen in the animations) draws the Toa from their respective crashed planets, upgrades them (at the same time, wiping out all of their memories), reseals them in their Toa canisters, redirects them to Okoto, and gives them a boost so that they can get their faster.
What of the Nuva symbols on the 2016 sets? some might ask.
Honestly, in conection with my theory, they would be symbols given to the Toa (that match their Nuva symbols by chance) that would give them new upgrade (2016 upgrade) and mastery over their elements.
My theory, as in depth as it is, still has some gaps like WHY DOES LEWA CONTROL PLANTS AND NOT AIR?!?! WHY LEGO?!?!