Visual character customization isn't necessary, though. Hundreds of games give you what there is and people play it nonetheless. When it isn't there, most people don't actively desire it. Removing it from TF2 at this point WOULD be drastic and bad, but I was responding to the overall idea of the thread "do it over" more than your actual goal of changing the game we have.
Reskins are actually the least of my concern. It is all the other ones that are extraneous and complicate the game. When you had only three weapons on a class, you knew exactly what you were dealing with when you prepare to engage the enemy you see ahead. That was part of mastering the game, learning how to handle each class vs each class. Having a single (maybe even two) good alternate weapon for each slot that provides a meaningful difference while staying within the archetype of the class still allows you to predict the coming encounter pretty well ("I think he has X, but there is a 30% chance he might be using Y, either way, I know what I'm dealing with"). When you have as many as we do now, you can have five of the same class on one team, and every one of them has a different loadout. There is simply too much to reasonably learn the nuances.
I could go on and on for pages about the sniper and spy, they are a sore spot, and you are echoing what people have said in the past. I'll try to keep my point short. Regardless of any alternate weapons, or specific ways to counter them in given situations, the very core of their archetypes are non-engagement combat. The sniper is supposed to kill you from too far to be seen. The spy is supposed to kill you without being detected. This is anti-engagement and anti-gameplay, literally. Their primary purpose is fulfilled when the enemy could not play against them. Games are meant to be played with and against people. Thus my ideal Team Fortress has 7 classes.
I guess a payload could be made simpler, but had it been invented later in the game's life when valve started hardcoding everything, I can only imagine how restrictive it would be and how many maps wouldn't exist because they relied on changing small things about the payload system. I don't think the actual game logic entities ever amount to significant edicts except when you are doing something really weird (me, Egan, Penguin). Even on payload, the path_tracks themselves are the extreme majority of game "logic" edicts.
I get that you can port a map successfully, it is just my personal opinion that the effort is better spent on a brand new map rather than "converting" a map that puts limitations on you, and might end up different enough that oldies won't care about it being a port because the nostalgia factor isn't there.
But... I really didn't want to get into a big discussion about this, because like I originally said, your goal seems to be drastically opposed to what I came into the thread thinking. I wasn't even expecting someone actually wanting to mod the game, just talk. You are seeking to add to and change the game to improve it, I feel it needs a pruning because there has already been too much unchecked growth. None of this really matters to your project.