players that are losing and then run the clock out.

I disagree. There are often critical moments in games of 15+ minutes where a player will legitimately spend more than 3 minutes calculating their next move. Something should be done about people who run down the clock, but I don't think this is the solution. Perhaps banning repeat offenders is the best solution rather than adding extra restrictions to games that will impact genuine players. 

I am reading the forum and waiting my oponent lost by time in a tournment (rapid 10)...

I know it is hard to define, but something must be done.

And if you open another tab with your login you will be kicked out. Be careful. LOL

lol I tried doing as suggested by another user and start a new game, then I lost the one the guy was stalling on. I don't mind too much about the points but it sucks when someone wants to draw (giving me a loss in points) 3 mins into a 30 minute because they say "Sorry I have to go". I just said ok resign and it's infuriating

The problem is, there is no way to distinguish between a player intentionally running out the clock, and a player simply taking a long time to find the move. This means there can't be some algorithm or something that detects players who do that illegally.

So I guess we just need to live with that.

But if they outright say "I have to leave" 5 mins in then don't resign. You just wait 25 minutes and say whatevs? There should be a nuke button which is only used when the person pressing the button is sure that the other player is intentionally stalling and have admitted it. Then anyone wanting to appeal a nuked game could do so. I'm just spitballing but surely theres another way than to just live with it.

That will simply create a new problem : players abusing this "nuke" button or even using it when they're losing. The only thing you can do is report the player who is stalling, I imagine that if the player is reported a lot, the administrators will intervene and take the necessary steps against them.

I thought in a solution for this problem.

If a player takes more than 2 minutes to move a piece, and then lose in time, the other player will be asked if the opponent was stalling.

If this behavior happens more times with this player, he can be punished.

It may work because this kind of player simply move to another tab in the computer and let the game run out of time. If there is any kind of punishment, it would not happen more.

To be honest, it happens in like 5% of the games, so maybe is not the bigger problem of the platform. Like, there are much more serious issues to deal.

This is not the case, the sport had fair play and sport spirit. If a behavior has the only purpose to harass the opponent, it should not be allowed.

As you can let the time runs off if it matters in a championship, as it can be considered rude or unsportsmanlike, at least it not for fun.

This discussion is not about freedom, it is about avoiding bad behavior that makes the community toxic. I see no reason to be against staling, as you see, chess.com have a report category to this behavior, so they agree it is harmful. 

I think this solution is already implemented in a way. After the game is over the site asks you if your opponent played fairly. I imagine if the same player gets lots of "No" feedbacks from other players, the staff may intervene.

Another problem is that your opponent may really not be stalling, even though he's taking a lot of time to play or even lose on time (say, he went to the toilet while leaving the game open, and it took him longer than he thought)

This is simply the fundamental problem with online chess : you simply can't know what your opponent is doing. 

An interesting solution that just came to my mind : if the stalling behavior consistently starts at the moment the player gets a really bad position (per engine's evaluation), we can say with confidence he's stalling on purpose.

Good idea. Always will be hard to verify it, but possible. It is a feature that can improve the community, I guess. But also, need to be implemented with caution, to not run in false positives, even if some toxic players have no punishment.

It would be nice if, before stalling, the person thinks that can cause his punishment and do not do it and resign.

I realize this kind of behavior is more common when the player lost a winning position, it makes anyone mad. 

If a player was in a really bad position, wouldn’t it require more time to find a solution?

Chess.com already has a policy in place: https://support.chess.com/article/675-what-is-stalling

Just report those players and move on.