If the Lannister-Baratheon dynasty and its major supporters survived the War of the Five Kings, how do you think Tywin’s “divide and rule” doctrine would have worked long term? How manageable would the Riverlands have been with the Freys in control of the Twins and Riverrun and the lord paramount based out of Harrenhal, or the North with the Lannister of Winterfell as lord paramount and the Dreadfort holding the title of Warden of the North, compared to the previous centralized models in each?

I don’t think it would have worked well:

• The Riverlands are going to be incredibly unstable, since the Freys are hated, over-extended (with half of their forces sent North, and the rest trying to hold the Twins, Riverrun, Darry, Seagard), and likely to face a rebellion. On top of that, the de jure Lord Paramount (who’s also Lord Protector of the Vale) is looking to overthrow the Lannister-Baratheon dynasty. 
• At the heart of the regime, the Tyrells want to become the power behind the throne as the Lannisters were for the Baratheons, which includes assassinating inconvenient monarchs to replace them with a compliant child monarch; the Martells want to violently overthrow the current regime and restore the Targaryens; and none of Tywin’s children want to cooperate in his plans, which means that there’s.
• The North is in a state of chaos, the Boltons are planning to betray the Lannisters when they get a chance while the Lannisters were planning to do the same to them, Stannis is in the field and slowly working towards an alliance with the Stark loyalists and the wildlings, etc. 
• The Ironborn aren’t in-pocket at all, and are destabilizing the whole system by attacking the Reach at the time when Tywin needs the Reach as his muscle.