If you look here there are a couple of alternatives to QWERTY, like Dvorak and Colemak. TNWMLC has an effort score of 5.6, or 86% more effort than QWERTY coming in at 3.0. Dvorak is 30% less effort at 2.1 and Colemak is 38% better at an effort score of 1.8. In other words, could be worse.
Even worse, there is clear evidence that the results were altered through a series of inappropriate data manipulations. For example, the initial typing scores for the QWERTY typists were measured differently from the initial scores of the Dvorak typists so as to greatly disadvantage the QWERTY results. The report states that, because three typists in the QWERTY group had initial net scores of zero words per minute (!), the beginning and ending speeds were calculated as the average of the first four typing tests and the average of the last four typing tests. This has the effect of raising the measured initial typing speed, and lowering the measured ending speed. In contrast, the initial experiment using Dvorak simply used the first and last test scores. Using numbers reported in the footnotes of the report, we were able to calculate that this truncation of the reported values at the beginning of the test reduced the measured increase in typing speed on the QWERTY keyboard by almost half. The effect of the truncation at the end of the measuring period also decreases the reported gains for the QWERTY typists, though the size of this distortion cannot be determined from the report. The important thing, however, is that the numbers appear to be cooked in favor of Dvorak.
Incorrect studies is one thing. The site I linked to uses a model to calculate finger distance traveled - here's how they calculate it and here are some other parameters. He runs all layout through about 15 books of typing to see what takes longer. I don't think Dvorak is great, but it is less effort / time to type. It's not good enough to warrant relearning typing from scratch for me, but that's a different discussion.
Yeah, I know. I don't believe in the site you linked. Ask a biomechanicist how many degrees of freedom the human hand has and you'll get a number between 21 and 27... and you have two of them. Throw arms in there and you've got another 6 or 7... x2. Your website only accounts for 16 parameters in its math. Statistically, they've oversimplified the model by a factor of five at least. A system that complex is best developed empirically, not theoretically, which means iterative testing. Iterative testing developed the QWERTY keyboard, less iterative testing developed the Dvorak keyboard. Empirical testing bears out that the QWERTY layout is better.
But it could be better! Unfortunately, getting used to a new keyboard layout is hard.