There's an interesting idea.
But I think instead of introducing him in a humanoid form, he ought to be an evil Alicorn, and the creator and first owner of the Alicorn Amulet.
And so the lore would be that he was the absolute ruler of all of Equestria before the Two sisters had even gotten their Cutie Marks. And the two of them managed to trick him into storing a portion of his powers in an Amulet, his pride being his downfall in making him weak enough for them to fight (Serriously, with the Elements the princesses are kind of weaksauce.) After he is defeated, he is banished to Tartarus, and, escaping at the same time Tirek did, he and Tirek would bide their time, scheming and biding their time, until the right moment. Cronus sent Tirek out to cause a fuss, create a distraction, to throw everyone off his scent while he tracked down the Amulet.
Depending on where the Amulet had been hidden by Zecora after Magic Duel (no doubt someplace deep in the Everfee Forest) either Cronos finds it on his own, or he makes an empty threat to trick the ponies to leading him to where it is hidden when they check if it's still there. Either way, he manages to get a hold of it, and resumes his role as "the rightful master of Equestria" after defeating Sunbutt and Moonbutt, casting both of them to opposite ends of Equestria, and imprisoning each of them there, in trap filled castles.
Twilight has to make the choice between rescuing Moonbutt or Sunbutt, as she can only reach one before Cronus returns from his conquering of the Crystal Empire.
She saves Celestia, but when they return to Ponyville, they discover that Cronos has allied with Sombra (who has been given a new body by Cronos) and Chrysalis, amassing an army of crystalized Changelings. Discord had been brought in to try and stop the threat again, but Cronos was powerful enough to make chaos itself bend to his will, and beat Discord at his own game before casting him into Tartarus. Where he is welcomed by a snarky comment from Tirek.
The mane 6 use their Harmony Forms to fight off the army of Crystal Changelings, banishing Sombra back into formless shadow, and imprisoning both Sombra And Chrysalis in Tartarus.
But even Harmony Forms can't stand up to Cronus' might, despite a kick-ass 6v1 battle of Harmony Beams against Cronus' horn lasers.
The mane 6 are defeated, and they flee before they are sent to Tartarus, Twilight teleporting them all away.
The rest of the season is spent on reuniting the other princesses and Discord (That episode would be fun, each pony having an important role to play in getting past the obstacles guarding Tartarus), going into hiding in the ruins of the Castle of the Two Sisters, where Twilight finds a notebook of Starswirl's, a load of spell theory and mostly gibberish to anyone but Twilight, even Celestia can't make sense of some of it, and various attempts at breaking Cronus' hold on Equestria, with little success.
In the finale, Twilight discovers a spell based on the notes in Starswirl's Notebook with some of her own theories, but they need a large number of ponies for it to work. The Princesses, the mane 6 and Discord make coordinated strikes against vital targets in Cronus' Empire, freeing large amounts of enthralled ponies. This Incites Cronus' Wrath and renews his hunt with improved vim and vigor., he is confronted by the Princesses, Discord and the mane 6, who distract them while Twilight casts her new spell.
Cronus' pride befalls him again, as his preference for an actual fight rather than easily defeating the helpless Twilight allows her to prepare her ultimate attack, drawing from everypony's friendship and affection to form the fearsome HARMONY BOMB!!!1!!2!!!!1!!1!11!!1(dubstep)
So Cronus gets loved and tolerated so hard, the Alicorn Amulet is broken, forever robbing him of his powers.
He is banished to Tartarus, and then there's a victorious song, and everything is sunshine and rainbows and everyone poops butterflies forever, the end. Series finale.