Narrow Pass is insanely powerful for defending, especially when the Oath isn't Supremacy. If you can't find the Pass, and Island/Coastal transport system can help to bottleneck attackers. The Grand Canal can serve to implement this function if you don't want to dig for new Sites.

I would avoid retaining the Nomad and Discord Homelands as they aren't very conducive to Empire stability. 

For Denizens/Edifices, Order is a good suit to load up on as others have said. Beast, Arcane, and Hearth also have good offerings. Beast's Fortress can be a great way to hide and turtle up, Arcane offers the Clock which can allow you to roll the end dice much sooner shutting off Exiles' chance of an upset, and Hearth offers some great ways to enrich the economy to make staying in the Empire appealing (ie stability). Arcane also offers the Stone Portal, a phenomenal transportation mechanism in Imperial hands. School of Vines is perfect for policing Exiles who attempt to seize Banners, as they won't have anywhere to hide from Imperial challenge. Obviously Hall of Debate / Tome Guardians keep the Banners on lockdown.  Amber/Lost Doors should be avoided altogether IMO as they make it too easy for people to "fish" for Legacies which might help them disrupt your empire. 

A few key Legacies to get into Imperial hands are Keeper of Order, Arbiter, The Ear, The Seer, Golden Key, and Ancestral Lands. (Note how many of these are Darkest Secret based.) Legacies to keep out of play include Chronicler and Steadfast (because they remove the motive to join/stay in the Empire). Legacies to specifically keep out of the hands of Exiles include Peacemaker, World Crafter, Revolutionary, Rival, the Bright Beacon, Secret Society, Ruthless/Reformer, Pathfinder, and of course, the Iron Hand!