A lot of great ideas in the original post. Here are some personal inputs I'd have:
- Hunger and Thirst
Just like obtaining a "Well Rested" status when you sleep on a bed in Fallout 3, if you don't eat 3 square meals a day and drink 3 bottles of water a day, you should get a "Starving" and "Dehydrated" status. Starving should reduce Stregnth and Endurance. Dehydration should reduce Agility and Perception.
- Stimpaks and Healing
Stimpaks should be RARE. Like, only available in very limited quantities for sale from clinics, or in Medical Kits in abandoned vaults. Crippled limbs should only be able to be healed by a doctor in a clinic. That way, if you get into a heavy fire fight, you need to limp back to the nearest settlement to get properly patched up. No more hiding behind a barrel and shooting up a Stimpak to heal that "crippled" leg!
Another very RARE item should be something called a "Self-Aid" kit that will heal crippled limbs ONLY and not regenerate health. These could be found for sale in doctor's clinics only, but are extremely expensive.
Stimpak healing effects should not be instantaneous, either. They should be treaded like other Chems in the game... you can only use them one at a time, and they have a time-limited duration. So say you're in need of healing. Now you can only shoot up one Stimpak, and it will heal X amount of hit points over X amount of real-time minutes. This will make you think twice before "Run n' Gun" tactics.
- Food and Drink
Food and drink should be uncommon, but not as rare as Stimpaks. Food/water will be the primary means of regenerating health. The healing properties should be instant, but in much smaller amount, the opposite of the Stimpak. They should still have a time-limited duration (so you don't eat 100 Iguana Bits to regen full health) to simulate being "full".
Rads should be increased in Food/Water considerably across the board. Standing in radiated water is one thing, ingesting it is a completly different thing! Also the Food Sanitizer should reduce the amount of Rads present in food, but not eliminate it completely.
Different foods should have a different "max healing amount". So less nutritious foods like Snack Cakes and Potato Crisps are more common in the game world, but heal less HP overall. Foods like Brahmin Steak and Iguana in a Stick may not be "less" common, but have a much higher rad count, yet heal more HP.
- Sleeping
Sleeping should heal X amount of HP per hour of sleep.
Just a few ideas I'd throw out there...