Considering the first three episodes have not even covered the original plot, three more episodes to get there, the last three with one being mostly an epic battle. Leaving nine episodes to cover the actual story progression.
Then you have to fit the flashbacks for the actual intro of the characters. When the story starts we do not even know who Tahu is and what he did. but that won't take too much time. That is the first season. Lets say that fine and we fit all that in the first season. Lets take a look at the second season. Now we have to cover a newly introduced character, Makuta. The civil war and how it got started, then progress that pot line while keeping track of Makuta's plans to use the brainwashed Toa. Then halfway or near the end we have to introduce the theme for the third and last act.Maybe adding an explanation on the three brothers if not just mere foreshadowing that they are not the only ones, one is cray-cray and that the "good" one was not as good as people thought. Which granted takes less time than the entire flashback set up for the first season. Then again this is the first time Matoran are going to be able to interact with their new Toa so we have that to deal with too. Tahu's arc and if he finishes his penance in this season or the next one. Kopaka's arc and what he will do as a Toa and a king, specially since he know little on how to govern and certainly does not have the emotional strength to "replace" his father, as well as the problems a Toa king can cause given how much power they have. Onua has to deal with loss, mayeb a death in his family as well as his unwillingness to fight on the war, and has to finds growth on it. Gali has to deal with fanatics or separatists. As well as her dilemma on a civil war considering she values unity, so she might have to help the Toa reconcile. Pahatu's arc, he has to deal with his trainer and finding that the entire frozen island was a bigger conspiracy (maybe), how fractured his region is, and how he has to maybe unite the interest of the merchant kings into the war. His entire region faces a big problem of unity. The merchant kings care about profit, they do not like each other. The entire region is in no condition to go into a war. So Pohatu has to make them ready while dealing with his trainer. Then you have Lewa. Which I have no clue were to start. She has to deal with her former "friend" being now an enemy and a monster. Returning to a society that idolizes her, being considered maybe a threat by the government and taking responsibility of being a Toa. Granted some of these can go to the third season, but this leaves little time for the Toa to interact properly in the second season A, leaving most of the romance developing on the second season B, Considering mos of them are strangers to each other, true romance is not a thing in season one A or B, maybe attraction. Second season A has no space, as they have to deal with their own region separately. Second season B maybe gets a chance to start it. Leaving actual romance to the third season A and B. If we start building it from first season we can get there for season three. Considering not even a years has passed between the first season A to the second season B.
Considering the transition to the third season was discussed to be an interruption of the civil war by Makuta's army, we can the third season in several ways:
- Time skip to after the Makuta invasion. Age of darkness, where the Toa are leading a rebellion in the shadows.
- Continue exactly where we left off. Either Makuta's army joins the fray or it already fought and the Toa have to deal with the results of that fight.
- Start with how Makuta got an army on the first place (if the army he has are not matoran of his cult.)
Either way this season is the one with the most space to have an actual romance develope, specially because ti allows for timeskips.
On a side note, I just realized second season A and B are going to be political intrigue with little action. I think we have to do it like Captain America: Winter Soldier. I do not have better examples of an action political intrigue story, that has been distributed as a moving picture.