Erm. It doesnt take a genius to figure it out. If the top doesnt play, they get moved down automatically after X amount of days. This has been a rule for a very long time, decades actually. Trying to come up with something new isnt warranted here. All your other stuff is great, but this aspect of it worked as advertised and is used by millions everywhere else because its just the best method
The current ladder doesnt have the timeouts like cases ladder did decades ago. It was a major flaw in recreating cases ladder. But everything else, they got right. There were rules that stated #1 had to play the #2 player within X time, same goes for #2 with #3, 4 or 5, and so on. As you got further down the ladder, the playing requirements got wider. Only the #1 spot had a requirement to play #2. Maybe thats where you could add some changes that would require #1 to play more than just #2 but #2 has to be in there for a reason. The time periods to play the other ranks could be longer than #2 for example. That would be a decent "improvement" if you want to try to improve things.
The only "flaw" in the timeout was that if #2 refused to play #1 (trying to get #1 via timeout rather than playing). In that instance there was actually a way to report it and if #2 couldnt refute the claim, the #1 player was not moved down. One method I thought of back when I hosted the ladder was an acknowledgement flag. If the #1 and #2 were online at the same time, the server sent them a notice saying that they needed to play. If one of the players didnt acknowledge the flag, they were penalized for it. This worked around both problems. It was implemented, but tinfoil hat morons caused problems that werent really necessary.
Maybe even disable a player's ability to join/create games until they accept their challenger's challenge and they either accept or they get moved down, their choice. They could always play on another name if they plan to just let it time out, so its not like you'd be killing their ability to play at all. They maybe tag their ladder name with the amount of "timeout penalties" it has received. Sort of a badge of dishonor for players who continually have timeouts (viewed the same way as "drops" in war2's stats).
My suggestion is to just work with the existing rung ladder and add the timeout features, its only a few lines anyway. Then think of a way to solve the problem of #2 refusing to play #1 (such as a server flag, server email, or something along those lines, the technical term for this solution in other games/ladders is called: Mandatory Challenge Acceptance). So as you can see, theres plenty of room for innovation with the ladder system without breaking it's "rung" system.
BTW, your "random.pud" feature. Great addition. Even if its not used for ladder play. You should consider making the pool of puds include the Kpuds. Its the only group of puds that actually had a "standard" in order to be considered a "Kpud". So they are ALL balanced perfectly unlike most of the built in maps and current customs maps. Most of the current players probably dont even know what a Kpud is (except those of us who were around on kahn/kali/zone where kpuds were the bomb lol) let alone what they look like, but every one of them would do well in them because they are all similar to current most played maps (GoW, PoS, HSC, FoC, etc). Only the customs players would struggle on a Kpud.
You also mentioned the old ladder still works. Have you checked it lately? It doesnt have a mysql connection
either that or I dont know the url for it haha. I looked at
https://ladder.war2.ru/ to see if it was still up
I think the last time I looked at it was probably 5 yrs ago or more
I dont play enough to care for it.