this was actually asked of James Dashner (the author) if he was ok with splitting Death Cure (the 3rd book). he didnt like the idea because that would ruin the pace of the last act, plus the obvious fact that where the heck would they even put the split in?
although for you O'brien-as-Spidey fans that isnt really good news

. Dashner is writing the 2nd book to the prequels of the Maze Runner trilogy and it features Thomas largely. its a big reason why im skeptical with the whole O'brien rumor because logistics-- where is he gonna fit Spidey, MR and TW in his schedule? unless he drops Teen Wolf.....