The quality of games where hit by what I have called the "Next Gen Boom" where everyone was immediately captivated by graphics, and this left less time, budget, and data resources to make a decent story and game mechanics.
Fallout 3 is an "Action-RPG", a Live Action (in this case, a FPS), and an RPG combination. FO3 does neither perfectly.
The RPG elements that need tweaking are of course the realism aspects. Enemies are bullet sponges, and so are you. On top of that, if you tweek the difficulty, it just becomes worse. Either you are too epic, or too brittle, and vice versa for enemies. Also, ammunition without weight has a primary problem that blends both generas. RPGs, especially a survival themed RPG, requires some form of inventory management, primarily weight, sometimes volume, and in FO3 this is gone for medical supplies and ammunition. As for an FPS, there are generally limits on how much ammunition you can carry for you're weapons. Also, there is a lack of flow. The game's quests don't really influence each other enough to really be called a story line. It's loosely ordered chaos. The game just feels like some of the side quests are out of place, and seem to be uninvolved in the beginning. If it was harder to get to the main part of the city, it would make you look around for supplies and ammo of high quality, and train to fight through the always mentioned HORDES of super mutants in the city, witch, obviously don't seem to exist in this game. Conversations also felt limiting and bland, not necessarily due to lack of options, but defiantly due to the total animation system, and a seemingly lacking involvement of the character. Mass Effect was good at this, but the main character doesn't need a voice.
As for the FPS elements, they are mostly simple. There is no real way to be tactical. Ubisoft is one company to look at. In Rainbow Six, the Cover System and combat feel, well, felt real. As for stealth mechanics, witch we all know are just plain broken, Splinter Cell felt a lot more like being a sneaky person. Enemies also didn't seem to react to noise. Tossing a rock to make a noise or tapping loudly on a wall would be nice, kinda like Metal Gear stuff. Distraction is a great method of Evasion. Also, smoke screens would have been nice. In Far Cry 2, the guns felt right. They would jam during a clip, instead of only when reloading, and you would loose that jammed bullet to the floor. And when you're gun broke, it blew up in your hands. (Witch would remind me of critical failures...)
The game also has a lack of common points to FO2. I understand not naming or even using some of the weapons due to copyright issues, but I know that some of those weapons weren't owned by actual companies. And SPECIAL, just like in Oblivion's system, got dumbed down. I understand that Bethesda is trying to focus on a broad market, but believe it or not. Even a casual player can handle substance... They are just pissing off the original market, sadly, but I do love you Bethesda.
All and all, there are a lot of ideas, but they would be repetitive of all the other previous ideas I, and others have posted.
P.S. Solar Scorcher would be nice.