Here are some changes that the mod will most likely have:
New gameplay focused much less on leveling up, although some sort of experience system will remain. Possible cover and melee system.
New models and textures to represent the Gears universe better.
Totally new items, from armor to food.
Little or none of the original Fallout story.
No radiation, instead there may be a sickness system.
Enclave replaced with the Locust and BoS replaced with the COG.
Up to 3 companions at a time.
Characters from the Gears universe such as Marcus, Dom, Cole, Carmine, etc.
A mix of Gears 1 and 2.
You may get to choose who you play as, have a few options, or have to play as Marcus.
Enemies replaced with their Gears counterparts (Deathclaws = Berserkers, Behemoths = Brumak, etc).
Most weapons from Gears 1 and 2 plus some makeshift weapons (baseball bats, tire iron, etc).
Hopefully a downing/reviving system, special exections and hostage taking (unlikely).
A possible item carry limit (limited ammo, limited guns, one suit of clothing at a time, etc).
A modified wasteland, both in names and some areas may be editted to fit better with Gears of War.
Possible new items with special functions (tac-com, Hammer of Dawn targeting tool, etc)
A new HUD, perhaps with a fade effect like in Gears of War.
Radio will be editted, hopefully with new music to fit Gears of War and Three-Dog will be replaced.
A possible squad system where you can get a whole new squad depending on your alliance.
A possible buoyancy system (you can sink if you're too heavy.
Visceral and brutal gameplay like in Gears of War.
Heavily modified player model and animations (you can see all your weapons on your character, they move different and have animations for any new features added in, perhaps even a slightly bulkier character to stay true to Gears of War).
No VATS.
Dogmeat replaced with JACK.
Possible mods for the DLC in later versions. Operation Anchorage becomes Pendulum Wars simulator, The Pitt becomes a Locust-run city with slaves and Broken Steel becomes another mission you can do with the COG army.
I urge you not to make a fangame, especially not something based off of Gears of War. Something original would be much better.
Alright, I have taken your opinion into consideration. I'll wait a while to see what other people have to say on it.
P.S. Technically it wouldn't be a fan game, but a mod :P