Bethesda puts in a tremendous amount of work making games that are excellent in their own right. But unfortunately, for any number of perfectly understandable (or at least generally excusable) reasons at the end of the day they product they deliver, while excellent, is still far shy of what it COULD have been.
I'd say that it should be taken as a complement (in general, the unoffical patches are a bit of a jab at Bethesda's QC team) that bethesda provides a framework good enough that hundreds of talented people are willing to add content to the games for free.
In many cases, this content simply couldn't have been put into the game for retail release. In my perusal of both Oblivion and Fallout 3 mods, I've found dozens of mods that exist for little other reason than to add some gratuitius nudity (or outright hardcore pornography) to a game. Other mods add content without regard to cannon, game balance or mechanics. But there are a few out there that produce mods that actually help bring the wasteland or Tameriel to life better than Bethesda managed. From a simple mod that makes the night sky more realistic through the use of actual high-res images of the nigh sky to mods that give characters a little more character in conversation.
In many cases, the limiting factor may simply have been technological. Few people have a super powerful gaming machine and thus don't have the graphics horsepower to spare rendering models wrapped in nothing but ultra-high resolution skins. Going from the vanilla version of fallout 3 set to ultra high to a version leveraging a lot of these new models and skins more than doubled my standard memory usage to nearly 3 gb.
In other cases, it might simpy be that they ran out of time. Bethesda, like any game company, needs to ship games by certain dates, and inevitably features and ideas get cut in the process to make sure the game ships.
I had almost forgotten why I loved playing PC games until I built myself a new machine and threw oblivion in the drive. Sure I enjoyed oblivion as much as one could expect when I played it on 360. But now I had access to more content than the game could ever have hoped to ship with.
