Ok, so here's my views on this:
I really think a line should be drawn at using loadouts, mainly because it helps gameplay immensely if you know precisely what every enemy you see can do, but also because it prevents us from going down a slippery slope whereby we end up implementing a load of bullshit into the game.
However that doesn't mean that we should just blindly go "stock is best" and leave it at that. If there was any weapons that we can agree helped the game it can be incorporated into the classes kit. There's really no need to implement alternative weapons for features that can easily be a core part of the class.
Here is my thought for the classes:
Personally I don't really don't care for any of the stuff this class was given over the years. I see some people vouch for the FaN, but I would rather the scout's mobility be just his double jump. People can feel free to put forward their arguments why the FaN was a good addition to the game though. As far as the wrap assassin goes, you could just implement a version of the sandman though just does damage instead of any sort of stun replacing his stock bat, but I really don't think that's necessary either though.
The only thing the soldier has received that I really like was the rocket-jump melee bonus given by the Market Gardener (reduce the damage though, a full crit is too much) and again, that doesn't need to be an extra weapon, just incorporate the feature into his regular shovel.
I've seen people argue that the Flaregun should replace his shotgun and I agree. The thing can easily be designed to fire underwater if that's a concern (makes no sense balancing classes around something so situation that most maps don't even have) and it makes far more sense as his secondary that his shotgun does. Would also like to see the axetinguisher's burning crit feature added to the stock fire axe. As far as switch times goes, I'd say have it so flaregun has a faster switch time but keep the axe at the default one.
Same as Soldier really, it could be cool if his bottle had a damage boost for when doing sticky jumping similar to the soldier's shovel.
I'm not really a fan of the GRU, but if people really feel the Heavy takes too long to get to the front line then maybe just a small buff to his shotgun/fists speed might be better (helps to make fighting with the shotgun more viable). I would like to see the original sandvich be part of his kit. But I think it's a really bad idea for any of the classes to lose their secondary weapon. I think it could work to have the sandvich by a right-click functionally of the shotgun. Just right-click with the shotgun out to take a few bites from the sandvich. No need for the sandvich drop mechanic, seems most of us agree that was a bad idea.
I see some talk about the Jag, maybe we could just make it the stats of the default wrench? I honestly think the Engineer works far better as a class when he is encouraged to play aggressively than defensively so I would welcome this. Having said that the mini sentries are the one thing I really don't want to see added to this mod. I also kind of like the rescue ranger and wouldn't mind seeing engie's pistol replaced with a sort of handgun that can repair buildings and grab them at a metal cost from a distance. His stock shotgun should remain his primary for fighting though. Also while I don't think the wrangler should be added to the game, I do think it could be cool if sentry-rocket jumping could be added. The way I see this working is have it so double right-clicking with a level 3 sentry built causes the sentry to fire it's rockets where you're aiming, no need for any of the other crap the wrangler introduces.
I occasionally see people say that the Kritzkrieg should be added, I feel that it defeats the main purpose of ubers in the game which is to provide a fail-safe for when the enemy team starts turtling with sentries, very annoying when you're dealing with a sentry nest and discover your team's medic is running a Kritzkrieg. And I don't really see what the weapon provides that justifies this. Generally I'm inclined to say that the medic doesn't need anything added to his kit.
I really liked the piercing shots that was introduced by the Machina and don't see any reason why it couldn't be a trait of his regular Sniper Rifle. No need to stop him from being able to fire unscoped, just make it so that the shot piercing only happens when you fire when scoped. Otherwise just keep him at stock.
I'm inclined to say keep him at stock. However I do think that being able to do headshots helps him immensely as a class. The problem is when it turns him into a mobile sniper instead of someone who is given an alternative way of stealthily killing someone. I kind of like how the ambassador originally worked, whereby you had to stand still to deliver the headshots.