Places aren't 100% looted because, well, what stuff was there worth steal that wasn't behind a locked door or container? NV has the same failing.
In NV, the stuff you can loot is generally either guarded by powerful prewar technology (RepConn, Sierra Madre, Big Empty), surrounded by hostile critters (ie Silver Peak mine), or already looted.
...Or already occupied by another faction who'd restocked everything with their own stuff, ala the Legion at Cottonwood cove or NCR at McCarran.
Simply because the game would be boring without finding something cool that no one else thought to touch.
In the original Fallout there was still stuff to loot, but it made sense. It was plausible that, say, the Toxic Caves went unlooted, seeing as how it was a golden gecko nest, had lots of radioactive waste everywhere, and had a locked door that needs an electronic lockpick to open. (And has a security robot with minigun and missiles down there to kill anyone who makes it through the geckos and and radiation.) The Sierra Army Depot was sealed up and also guarded by minigun turrets and armed robots.
The Glow still had a plasma rifle to loot because it was dangerously radioactive and had robots guarding it. It made
sense for these sites to be unlooted.
Compare FO3, where there's guns and armor just lying around for the taking. Lots of guns and armor. Two hundred years after the bombs fell, there's still guns and armor that have rested right where their owner fell.
People saying there is no farms etc, isn't there a Brahmin farm in Arefu, Paradise Falls, Megaton, Republic of Dave and there may be a few other places that hold Brahmin in pens and actually have them roasting on barbies but I can't remember off the top of my head. So that to me seems like a valid for of food production, though I see no crop farms but vegi's aren't the 1st things you want since they can take months to grow. There is a pretty large population of cannibals roaming the CW, Andale, The Hunters and the Vampire group living near Arefu could be classed as minor cannibals.
A handful of Brahmin isn't exactly enough to feed everyone in the capital wasteland. Particularly all those raider bands. Doubly so when the entire plot revolves around how there's no clean water.
It's not just farms either. There's a lack of any sort of industry. Where does Talon Company get their snazzy black combat armor and military-grade weaponry (including artillery!?) Where does the Brotherhood get so much obsolete power armor? Where do Overlords get their gatling lasers and tribeams?
All of this is just a symptom of the real problem though. FO3's worldbuilding simply isn't that good. They made a place that's fun to explore, but which makes no sense. Take Talon Company as an example. We know almost nothing about them. Why do mercenaries randomly hunt down people who give water to beggars? Where do they get prewar guns? Why are mercs automatically hostile to everyone they see, even though they're axing potential customers? Now, you can come up with plenty of fan-theories to explain their behavior (my personal favorite is that they're backed by the Enclave), but it's terrible worldbuilding to have not even a hint of the why of things in your setting.
The raiders are another issue. There's just so many of them, everywhere. Where does their food come from? There's not much trade between the various settlements in the Mojave. Where do their guns and bullets come from? The Pitt? What do they trade to get that gear? How do these people get enough water to survive when the entire plot revolves around how there's no clean water?
Muties have the same problems with food and water, but they also have a problem with motivation. In FO1 the muties had a reason to do everything they did - they had the Master telling them to. (We also see here that mutants are developed characters in their own right rather than being mindless killing machines.) In FO3, there's no mutant leader. It's like they just do things for lulz. It's poor worldbuilding to put all these factions in the game but not give them any motivations.
And this isn't even getting into lulzy things like the Rube Goldberg machine in the grocery store, the Dunwich building, or the teddy bear that spawns a mutie behemoth.