Having doctrines that you choose beforehand allows relic to expand on doctrines and make them impact the game even further than before. They can easily create 3 different styles and approaches to each faction and since only 2 factions will be featured in the game that variety will make it easier for new players/more casual players to play the game without getting bored at lack of content.
Sure it creates more match ups and make the game harder to balance, but the positive side of that is more creativity and variety can be put into the doctrines.
Well I don't think they're doctrines. Something seperate, extra, a modifier. Doctrines from what little i've been piecing together will still be chosen ingame and all that.