I was going to post in the old thread but it vanished. Here is a new thread focused on the important part. No complaining about specific games or players here please, just suggestions for how to make the world a better place, and discussions of suggestions.
* Time-out rule *
I think that an honest, reasonable player should never be in a situation where they have to play a Copper to extend how much time they have to think. I mean that's obviously bad. If there's a time-out at all, it shouldn't be based on when you last played a card. I think I would base it on how much total time the program has spent waiting for you compared to your opponent, with a threshold. For example, just an example, maybe you get to take twice as much time as your opponent, or 10 minutes, whichever is more. Probably with a warning before the first time it gives them the chance to eject you.
Obv. existing game logs could be looked at to see how often a candidate rule would kick in, and tweak it to be something that mostly would not happen except when slow-rolled or that phone call lasts a while. If existing game logs don't store enough time information to do that, they could be changed to store the extra information, and then data could accumulate. There are a lot of games per day, so, the next day you've got your data and can pick the best rule.
Both players get to stare at the board at once on turn one, but it's someone's turn. The rule should be generous enough that typically no-one worries about that. You could potentially try to special-case this - players click "ready" at the start, and have 3 minutes to do it (or are automatically "ready"), and this time doesn't count for anyone. But in the end some people will want to stare for a while and sometimes they will go first. It's nicer not to have to click "ready" at the start. I dunno.
* Matchmaking *
There is a separate but related issue of just not wanting slow opponents, even non-slow-rolling ones. I think that's reasonable. I would add speed as a matchmaking criteria (or, a thing reported to you when a match is made, that you have to okay to actually play the match). You could split it up into speed for the first and last two turns, and speed for other turns.
I think people who are not super slow will appreciate not being paired against super slow players. I think super slow players are not entitled to make opponents suffer through slow games or resign. Net happiness goes up if you can just avoid the match. If there are too many matchmaking settings, it may take longer to find matches; that seems moot here. If all you can get is pain, you can accept it or be happy not to experience it. If you are not getting matched you can lower your standards; if you see an offer and it looks bad you can decide to do it or not.
* Bots step in *
I don't think there's any way to stop someone from creating a new account, playing what appears to be a normal game, and then, if they're losing, waiting out the clock to give the finger to their opponent. Or, being a seemingly reasonable player for a while and then one day losing their mind and letting the clock run out on a late turn.
I do have a thing to try here though, or at least, a thought experiment. Once there are good bots, it could be that you could let a bot take over for you, and get the win (or loss), provided that it looks like you have the game locked up. Bots do not mind getting slow-rolled, they can sit there and wait patiently.
We can see if you're winning by having you click a button, "I think I've locked this one up," and the program simulates 100 games from this point on, with all bots (again, this requires that the bots be good). If you win all 100 then it lets you replace yourself with a bot and count the result for yourself (and if not the button is gone for this game, you just get one shot at it). However then you could just have bots finish all your locked-in wins for you and uh I dunno. Maybe it's okay - if they haven't resigned because they want to see what their deck does, well they can see that vs. a bot. I dunno what people would think of it though, and if they didn't like it, well it's impossible to test "is someone slow-rolling you" in order to confine it to that situation. So. A thing to think about.