Remove the random dragon spawns after you finish the quest 'Dragonslayer'.
Nothing more annoying than traversing the lands of Skyrim, collecting ingredients, roleplaying (yes I roleplay), clearing caves, and then... you hear it.... 'RRAWWRRSRASWRG'..... "[censored], not again!" An ancient dragon appears looking strangely identical to the last 50 dragons you encountered to get to this cave. After shouting it down with Dragonrend, what could of been an epic dragon fight is just you spamming the 'thwack' button on his face. Who knows, maybe you will get a slightly buggy kill animation.
Or maybe I want to fast travel from Riften to Solitude? BANG! Ancient dragon comes down burning guards and non-essential NPCs. This is probably the worst part. An NPC dying is like having my pet dog die. I cherish them all but for some reason Bethesda thought it OK to allow Vittoria Vici and Beirand to draw out a dagger and man-up to the mighty dragon. Eventually being killed. And forcing me to reload.
Skyrim was meant to be about the dragons. So why are they such an eyesore? I know it's hard to make something look really nice while flying but come on. If they didn't have dragons spawn at random and kept it confined to burial sites and Walls of Power they could program the dragon to move between set spots in the area, rather than flying upside down over there, then nosediving back over here.
Also, make them more of a challenge. No, not just raise the stats and be done with it. Improve AI and animations to make a dragon fight unforgettable.
I honestly have nothing else to say as this is my only real quarrel with Skyrim.