If a scoring system doesn't match the user's valuation, it will be ignored.
That is simply not true. I have some experience in this area, as I'm the main tester for the Repton series, and I've had some in-depth discussions of scoring systems for new versions with Richard Hanson, the series' lead developer. The main point of having a scoring system (in Repton -- I'll revert to Lemmings further down) is to reward skilful play, give the player a sense of what can be achieved so they can challenge themselves, and allow players to compete and compare their results with others. Expressing this as a single number is psychologically satisfying and makes comparison easy, without precluding specific challenges like completing certain levels without taking a time capsule.
Having a scoring system means that we have to make some decisions about numerical values -- e.g. a diamond is worth 5 points, killing a monster is worth 20. This is never going to "match the user's valuation", because everyone who's played the game knows that some monsters are extremely easy to kill, and there are some levels you can almost complete, but there's one last diamond that's always the problem. But regardless of what scoring system ends up being chosen, I know that in each new game that comes out, I'm just going to compete to try to get the highest score I can within that system.
Lemmings (except SNES) has always had number saved as the only metric actually scored, and I've enjoyed playing to try to save as many as possible. But I think for a new game, it would be more interesting to have a scoring system that incorporated other features.
When ranking lemmings first, then skills, then time, it is easy to compare solutions at a glance before they are even executed.
Yes: certainly an advantage to an even simpler system. But the downside is that it prioritises just one element of gameplay and makes all others nearly irrelevant. Whether the advantage outweighs the downside is a matter of taste.
I don't see any other use of mashing everything into a single number, because the player doesn't think like this at all.
Numerical scoring systems have been part of computer gaming since the beginning, so there must be a reason they've stuck around so long. (I think the main reasons are, as I said, psychological satisfaction and ease of comparison.) And don't tell me how I do or do not think. That's plain rude.
Also, time limits are not the norm any more in contemporary level design, except where it's the only way to fix backroutes. Compute solution times as if there were no time limit, counting up from zero.
The question of whether there should be a limit for time scoring is entirely separate from the issue of time limits in gameplay. A time limit in scoring is useful because it allows a scoring system to be tailored to the majority of levels, while still allowing exceptional levels (like Tribute to Benny Hill) to exist without time ending up overwhelming other factors.
As for time limits in gameplay, I don't want to go over old arguments again. I'll just say that there is no "norm". We all have different tastes. You've made yours clear, and for my contributions to the Lix community set, I've gone along with that to the extent of removing time limits except where I felt particularly strongly that I wanted to keep them. I think I would have kept more if I'd been making a custom pack by myself, because that suits the style of gameplay I prefer. I wish you would stop saying that my tastes are somehow "wrong".