My history with leveling mods has been pretty much to install them, create a character (or bring out a saved character, if the mod will seamlessly work with one), look at their stats, think something like, "What the heck is that? Why does my pure melee fighter have less strength and more intelligence? How did I spontaneously gain three levels?" and disable the mod and go back to vanilla leveling.
I'm not overly fond of the vanilla leveling system, but after a couple of years and dozens of characters, I have a clear enough understanding of how it works that I can almost always work around its problems.
Not nearly so much experience as Gpstr, but this is pretty much where I stand too. I only tried Realistic Levelling briefly, might have installed one other one very briefly. I keep playing with Vanilla Levelling.
The system has its flaws, but I've come to the conclusion that it is actually less random and poorly thought-out than is sometimes argued. From my perspective, I think the main problems with the vanilla leveling are as follows:
1) The game rewards me for tedious repetitive actions that some how just don't make sense. Sure, doing math problems all day might increase might math ability, but could I just do that to become a Master Mathmetician? Likewise, it just doesn't make total sense that I can effectively become a Master Illusionist or Restorationist or Alterationist simply by casing Starlight, Heal, or Protect repeatedly for days on end. This to me is the most egregious problem in the system in that it breaks immersion and makes it the expeience feel "gamey" instead of fascinating. True, if a player feels this way, he could just not do it, but then where is the boundary? If I cast Heal one extra time after a battle is that overstepping it? What about if my character starts his day by casting a nice refreshing Fortify Fatigue spell, does that constitute an action somewhere in the grey area between gameyness/clever strategy/roleplaying? It behooves the designer to anticipate precisely these patterns of player behavior and to include simple game mechanics that prevent the breakdown of immersion, not by requiring a player to voluntarily avoid 'cheating' but simply making it costly, impractical, or unappealing from a story standpoint. Not knowing the engine, I have no idea if it would've been simple to do, but ideas that come to me for how this could've been implemented: the background maths keep track of how often you use a skill within a given span of time, and simply award you diminishing experience as you do it more and more repetitively in a short span of time. Ideally, the engine would calculate if casting a particular spell were being done "under fire" and award full XP in those instances, but diminishing XP when it is being overused in practice sessions. Granted, most of the solutions start to seem pretty complex, let alone considering how complicated it might be to code them, but that is my take on that point.
2. Super-powered Goblins are as already said, annoying.
3. I never play with the standard classes, and do find that having an "area" (Combat, Magic, Stealth) of focus as well as the attribute specs makes pretty good sense from the standpoint of a more-or-less "classless" rpg system. I agree that a less-class-rigid system is the way to go, but I don't find the restrictions of the "class" system to be that annoying as long as I use custom classes.
4. Levelling up too fast as a result of actually USING your Majors, and thus be prevented from being a generalist. Given the game portrays the protagonist as a lone adventurer, this to me is a somewhat incongruous structure, though I can understand if they made it this way to make it approachable for the general consumer public. The resulting consequence for those who want to play a genealist with vanilla = Playing a Magic user with Majors like "Blunt, Heavy Armor, Armorer, Marksman, etc." is certainly workable but again, breaks immersion and the roleplay aura.
Other than that I think Vanilla leveling works fine.