This is just a random thought, This may be utterly impossible (like moving vehicals) but I'm posting it in the off-chance it's not. I'm not a modder in any way at all. I'm an idea person, I leave it to modders to chose whether or not to create what I think of.
How the Footprints Could Be Modeled
Using a software like Blender or Studio Max,
Load up the creature/human your making a footprint for.
Then edit them to just feet (Or whatever they move on),
Now I've not tried this but I can imagine that the "Ankle/Leg" (Top of the foot) area is hollow/see-thru
To fix that I'd suggest flipping the feet upside down to where your looking at the bottoms.
Now you have a left and right footprint.
Note: From guessing I'd say the left-side foot would become the right-side footprint, and vis versa.
How They Could Appear In-Game
Now I know nothing of the G.E.C.K, so I'm skipping the part of making each footprint a seperate object.
Also Two very skilled modders suggested two new ways to make them so scroll down for thier explanations.
Anyways, Continuing along.
Assuming its a static object in game now.
I'd suggest a series of scripts or a singular extended script
A Script that tells the game if the PC is within a reasonable distance (So that populated cells arn't covered in footprints, and thus also affect game-speed and clutter)
A Script that that identifies what terrian type the trackable creature is walking on (So you don't have footprints in solid roads/concrete/inside)
A Script based on PC Survival skill that either decreases that amount of footprints left behind or increases (So a Survival skill of 20 makes it very hard to find footprints and track/sneak up on enemies, While with a Survival skill of 100 you can follow them very easily and sneak up on them.)
A Script that identifies footprints to the correct creatures. (So a centaur won't leave power armor footprints.)
A Script to make the footprints fade over time (Maybe similar to what happens to gun shells)
Optional: A Script that makes only naturally hostile enemies leave footprints (so you only can track things that would normally attack you first)
Examples Of Possible Footprints
A Glowing footprint for Glowing Ones and Troopers.
Dragging marks for centaurs.
Sludge Spots for Ghouls And Ferals
Large bare feet with cracks for Super mutants.
Boot Prints for NCR Military/Legion
Shoe prints for normal humans/Raiders (bloody prints)
Large shoe like prints with cracks for Power Armored Troops/Brotherhood
Method Suggestions By Skilled Modders
Method Suggested by TallgeeseIV
I think I know of a better way to place them in game too.
There isn't really a script function to identify terrain, but... what you could do, is set it so, while you have a perk, or certain high skill, some sort of requirement. It runs a script on every npc/creature in the cell with you.
That script would place an explosion every few seconds, only while the npc/creature is moving. The explosion would be invisible, no damage, no force, nothing, and have a customized impactset, depending on the type of creature or npc, much like the different bullets make different holes in-game.
Then, instead of these explosions creating a scorch mark on the ground, you replace it with a texture of the footprints of a left foot and right foot slightly in front, or vice versa, doesn't matter.
Impactsets do get to change decals based on the terrain they hit, you just make the explosion do nothing unless you're on dirt (which includes grass and sand in-game)
And Viola! You now have footprints that you can track. Just like Red Dead Redemption.
Alternative Method Suggested by Gizmo
How about a script that places just the decal of two prints at the location and heading of the entity making the prints; and does this every time it moves.
These decals would fade with time, but be track-able by sight.