As my dragons are ALL spellcasters and an adult red gets up to 5 5th level spells they typically have at least one spell to guard the lair or make access difficult. For example, one of my Reds specialized in teleportation magics and most of the lair could only be accessed by teleporting, passwall, gaseous form, etc... One ancient Dragon had Finger of Death as a spell - just so that it could create hordes of zombie servants. Private Sanctum also can provide the PCs with a bit of a surprise when they try to teleport away from the dragon...
I like to have a flaw born of their overconfidence in each dragon lair. Something the PCs can (but not necessarily will) find and exploit that the dragon would not bother defending against because it is so overconfident. Stalagtites hanging over his head, a Dragonslayer sword in his hoard, etc...
I find that dragons are pretty fun as hit and run enemies, so I like their lairs to have mazelike elements, especially three dimensional mazelike elements. Having a dragon fly through a hole in the room and disappear for three rounds... only to burst up through the floor can be an evocative and surprising element. I want the fight with the dragon to be a long and savory combat where the PCs experience a lot of different elements rather than just a foe that stands toe to toe that breathes whenever possible and swipes with natural weapons while waiting to recharge.
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