Back to the redesigned plot: I would have the story progress as normal with some minor confrontations with Team Magma and Aqua, respectively, throughout the different towns and routes, casting a shadow from the moment of final suspense. Basically there would be hints and clues leading up to the final battle with the respective team leader and the eventual battle with Groudon/Kyogre. After the E4 you are congratulated on how far you came and such but the last test of strength would be the ultimate battle.
Catchin' lv. 70 legendaries that know Rest is indeed more challenging than someone with a full team'a lv. 70-75 Pokes... 'Specially when all of 'em easily fall to potent Fire STAB. Steven certainly was a disappointment. Good thing he isn't the pinnacle, ultimate challenge of the player's journey though; the Battle Frontier is.