The other day as I was wandering through Riverhold, a blood dragon attacked and ended up killing off Alvor, the very first NPC i encountered, and a reliable merchant for unloading loot. It was upsetting because it essentially diminishes the value of the town as a general-purpose stop, leaving only one other dedicated merchant (golden claw dude) who may also possibly end up outside and vulnerable to dragon attack. Later, an NPC outside of riften was roasted while defending his farm from a frost dragon with his bare fists, and i couldn't help but wonder if he would have offered an interesting side quest for me.
My problem is, once you initiate the dragon spawning portion of the main quest, they start showing up EVERYWHERE, killing merchants, potential quest givers, and other flavor npcs that i'd rather have alive. And since it never stops, i'd imagine that eventually you'd have ghost towns without any useful NPCs at all. I wish the NPCs, even the non-essential ones, would either run from attacking dragons or be unable to die from dragon damage, instead falling down into recovery mode like essential npcs (but ONLY under dragon attack... they would be capable of dying by the player or any other encounter).
To those of you with higher level characters, does this become a noticeable problem the farther you progress? I'm considering just creating characters that never embark upon the main quest, in order to preserve the full flavor of the game world. It's kind of a shame.