Carplos:
All my tests were with a 24-team league using a 162-game schedule. So technically, I haven't tried it with a MLB-sized league

My guess is that there wouldn't be any real change in a league as small as 16 teams or as big as 32. Beyond that, there might be some changes, but I wouldn't think they'd be too big.
Lighthouse:
I tweaked the MLEs because I wanted a three-tier minors system; I know it's more realistic, but 5 levels of minors felt a little like bloat. That being the case, I didn't think it would be best to plug the default single-A settings from the game into my lowest minor league, since Markus had made the rookie and Short-Season-A settings lower than A ball. I was concerned that it would make development occur too soon. So I just averaged the default single-A settings with the default rookie settings and used those for my single A settings. Given that I was using custom settings for the low minors, I didn't want the jump to AA to be too severe, so I used the default AAA settings for AAA and then just averaged the default AAA and my custom A settings for AA. That way the jump from AAA to the majors was the same as Markus intended and the jumps up the minor leagues were all smooth and even.
It's probably worth noting that I used these MLEs in the leagues that became both the default and recommended lines. As such it taints my comparison a bit, since "default" isn't truly default. Still... I don't think that it was my MLEs that threw the baseline off of MLB actuals, so the tweaks should still constitute an improvement.