STALKER is a much better FPS with awesome guns and a laughable storyline with minor RPG elements (only equipment and upgrades)
Fallout 3 is a shocking FPS with awful guns and a cool storyline with major RPG elements (Oblivion with guns)
STALKER's gameplay is realistic, bullet physics are incorporated and you spend a lot of time sneaking around groups of enemies or running from monsters.
Fallout 3's gameplay is a bit.. well.. easy. Sneak is overpowered, VATS is overpowered, Damage resistance can get ridiculously high, ammo doesn't weigh anything, stimpaks are everywhere and a good player can get every skill to 100.
STALKER has amazing environments that are quite explorable, you can even climb a few things and sometimes find secret stashes in attics and stuff. The map is split into bits, with annoying chokepoints to get to different areas. The buildings are very well suited for the gameplay, but in some instances they wouldn't make much sense in the real world and are a bit linear and bare.
Fallout 3 has amazing environments that are quite explorable, every single house has a secret stash in it (bad thing). HUGE map with no loading screens and even though they reused a lot of static houses and interiors the loot and layout is different in every single one, you can tell a lot of care went into every block of Fallout 3's environment. There are a lot more places to explore and secrets to find.
STALKER's wasteland is harsh, scary and dark
Fallout 3's wasteland is not.. but it's soooo pretty
They both have a very active modding community.
I was part of a major mod for stalker so I am a bit biased when I say STALKER is easier to mod.
They are both full of glitches.
They both have strange NPC behavior.
In conclusion, a glitch-free combination of the two games would be the best game ever made and would bring peace to the world (no time for war, everyone would be inside playing it)