I think this is a very good topic.
I think my JOEverse is pretty realistic nowadays, but back when I was younger I did have a bit more 'looser' universe.
Since one played with the figures that one had, it wasn't difficult to have the JOEs, Star Wars, Buck Rogers, and other lines crossing over. Snake-Eyes and Storm Shadow sparred with Luke Skywalker, while Wild Bill flew the Millenium Falcon when Han was in carbonite.
If I remember right, I think I had the JOEs entering some sort of inter-galactic transporter that moved them from Earth into space. Boy am I glad there wasn't any movie to come along that was like that!
[looks at Stargate]

As I've said before, I was always more of a Marvel guy than a Cartoon guy. Nothing more than I didn't get the channel from NYC (Channel 11?) that carried it.
That said, I don't think everyone has laser pistols or rifles. Flash has a laser rifle that is more of a work industry laser. Sci-Fi has the next-gen version. The Laser-Vipers have two different types: one to cut and one to target designate.
Snake-Eyes is not super-human. He is an extremely dedicated soldier who is proficient in many skills. He is a commando first, and a ninja second. He straddles both worlds, using the skills learned from both sides to make him who he is. He is not a member of every single subteam and is used on the missions that require him.
Hawk is the head of the GIJOE team, whether it's a 13 person squad or the bigger unit.
Duke is an old warhorse that realizes he is nearing the end of his military career. He wants to be the field leader and not just a desk jockey, but is gradually seeing the need for the next wave of JOEs.
It might be blasphemy to some, but Alpine and Bazooka don't go on missions together. I have never understood why an anti-tank guy would be paired up with a mountain climber. I can see them as teammates that reported to the JOEs at the same time and are good friends in the barracks at HQ.
Cobra Commander is a serious threat. He can not be trusted and uses every means necessary to achieve his goals. He has studied the famous leaders of history and shares many of the same traits, even if he fails to think he does. Like every bad villain, he has no problems shooting the messenger, shooting underlings for no reason, and using intimidation tactics on her subordinates. He is a cross of the comics and the cartoon, meaning he is driven like the comics but his plans fail like the cartoon. His major flaw is that he has no formal military training and thinks he knows everything about tactics & strategy. He's just a former used car slaeman from Springfield that was driven to fight back. This has to be this way so that there is tension in Cobra whenever Serpentor (the very symbol of military leadership. strategy, & tactics) comes around.
I think many of us have looked at some of the various characters and have come up with own way of using them (see thread title) or making them acceptable/believable.
I think that my universe is pretty tame and realistic, although with some suspension of disbelief. I strive for realism to the point I had to explain to myself where all the new JOEs come from-that's where my idea for the GIJOE Recruiter and the GIJOE Recruitment Reserves came from.
I look at each character and decide how to use them. For some there is only one 'look' for them. For example, Duke will mostly always be wearing his v1 uniform. However, I could see him is a Class A uniform for more formal situations, or wearing appropriate gear in certain environs (cold weather jacket over the v1 uniform). Ace will only be the pilot of the Skystriker, any other versions are different pilots (gray Ace is the Skystriker RIO, the F-16 one is a new character). There is only one Lifeline and anyone with the same codename (Sky Patrol Airborne, SideTrack vs Sidetrack, the two Long Range's, Thunderwing) is given a different one to avoid confusion. Bio-Vipers, Monstro-Vipers, and the Venom troops are limited in operation-they are more of lab accidents (the stuff of horror movies). Any of the surgically altered Cobra troops are okay (Strato-Viper, Hydro-Viper, etc). Croc Master v2 is wearing green body paint to blend in with the crocs. Serpentor is usable, given he's created from recovered DNA, but all his combined memories and thoughts are not real-they are historical notes he was subjected to while in the cloning vat (like Blanka in the Streetfighter movie). Robo-Joe. Robo-Joe is just a guy that has some prosthetic appendages and some computer interfaces that enable him to have movement (sort of a cross between a good unpowered Darth Vader and the six Million Dollar Man). I think he's more of a disabled soldier given the opportunity to be of use again. Dr. Mindbender v2 is more of a suit that has a bunch of tech gear that allows him to work in the field rather than cybernetic implants. There is no Lunatrix aliens or Cobra-La. Well, maybe Cobra-La if it is more of a 'cult' that dresses funny (think a non-powered Hellfire Club, cosplay, or the people that surgically turn themselves into animals) and is 'brainwashing' converts into thinking there are an ancient race.
Many of the vehicles do require the some adjusting to fit in. Many are awesome designs, while others are just meh...
-Destro's AGP (not 'anti-gravity' but powerful engines)
-SHARC: classic design, but used mostly 99% as a mini-sub. 1% Flying (flys and dives like jet skis do)
-Trubble Bubble: powerful engines for short flights and minimum ceilings
-Sky Hawk: nice design, but unrealistic. The 'bumblebee' of the JOE motor pool
-POGO: neat design, but rough on teeth and stomachs. I think it could be used as a cross between a Super Battle Droid and a Spider Droid for the BATs
-Sea Slug: only used as a water vehicle. No gliders.
-MCC: Won't fit in a C-5 to transport, so must be shipped by roll on/roll off Navy ships. Usually disguised as a building and only moves for defense purposes (disguise lost and imminent threat of destruction)
-BF 2000 Future Fortress: never used, 6 vehicles vs 1 Fortress? I'll take the vehicles
-Despoiler: sorta Destro's version of an air chariot...meh
-Arctic Blast: open cockpit cold weather vehicle? Hello, Blockbuster!
-Condor: Cobra experimental plane-not meant for combat
-Evader: modded motorcyle
-Razorback-based off of a construction vehicle like the Earthquake
-Mudfighter: more of an experimental plane
-Dominator: a tank/helo combo? not used
-General: used as a land version of the TTBP
-Retaliator: not used-Updraft flies the Locust (Dragonfly), or the one-man Locust
-Fort America: Ugggh! Clutch actually made this from salvaged junk parts and turned it into a fountain
-Patriot: so-so idea, but needs better tracks and propulsion
-1992 HQ: folding wings? not really used
-Armorbot: Destro saw ROTJ and wanted a chicken walker for MARS to sell
-Ninja Force ones: stationary training aids/parade floats
I guess that I am of two minds.
1) I want to have every member of the team be alive and all the vehicles in use
but
2) I have to accept that there are age issues, limited years allowed to serve in the military, injuries, teammembers coming in, teammembers leaving, etc. That's where the realism comes from.
And the fun of customizing and creating new characters!
I think I do accept some crossover ideas, as long as they are grounded in some form of reality.
-The JOEs could work with Scooby-Do, but he doesn't talk (more like Junkyard or Order) and the gang is more of a serious/credible team of experts. Not cartoony in any way, but could even be called, "Agent Fred ______, Agent Daphne ________, Agent Velma ______"
-Freddy Krueger and Jason could exist, but they aren't supernatural. They are just two serial killers with a penchant for melodrama and costumes.
-Stargate is just a theory. No active fields troops or trips.
Doc Brown could be a scientist/inventor that is kidnapped by Cobra. No time travel, no flying DeLoreans, and no hoverboards.
-There are no mutants with superpowers, however I can accept people that are born different due to some genetic chance of fate (extra fingers, siamese twins, etc)
-I can accept individuals like the Punisher, Black Widow, and other
non-powered individuals. If they are trained by the military or other agencies, yes. If they use any type of mechanical devices (Scorpion, etc), or have a meta-gene (Black Canary), or are based on mythology (Thor, Wonder Woman)-no. No aliens from doomed planets, no themed costume vigilantes (Batman).
-Professor Henry Jones Jr could be referred to as an author of a textbook or an old college lecturer. Used for information. Could even be brought in to discuss his OSS war service or talk about a specific situation he encountered in his youth that the JOEs are looking into because of Cobra. No magic, no supernatural stuff...
-Lara Croft Tomb Raider brought in for archeological expertise. Again, no supernatural stuff, no magic, no T-Rex dinosaurs.
-Movies and TV shows can be referenced, either as entertainment or as 'real' depending on the situation. Example: Ghostbusters could be the informal nickname of some guys from NYC (like the Mythbusters) that do paranormal research. Whatever 'ghost hunting' gear they might have is untested, they mostly just do investigative work. The events of the movie haven't happened and probably won't-it's the idea they are in the same universe.
Or JOEs going to Hawaii and meeting a certain Detroit Tigers ballcap wearing PI that drives a red Ferrari.
Or a few of the JOEs that served in Viet Nam interacted with the guys from Platoon, Full Metal Jacket, and Tour of Duty.
-Jake Grafton from the Stephen Coonts novels is one of the Jugglers.
-Dale Brown's main character McLanahan(sp?) helped develop the X-19 for the JOEs.
-Doc Savage and his group could be a thinktank. He's called the 'Man of Bronze' because of his fondness for sunbathing.
-Mack Bolan met Snake-Eyes, Storm Shadow, Stalker, and Wade Collins in Viet Nam. They also met Nile Barrabas too.
-James Bond can either be a book series, a movie series, or a fellow agent.
If a fellow agent, then substitute Cobra for Spectre:
"Do you expect me to talk, Baroness?"
"No, Commander Bond, Dahling, I expect you to die!"
(Personally I think 007 invading one of Cobra's over the top HQ's from the cartoon would be cool)
It's just liking something and then finding a plausible way to fit it in, even if it does conveniently ignore some aspects. Throw in the Hobbits, even if it means having the JOEs driving past a movie theatre and seeing fans in costumes.
-No Transformers.