I cannot agree with you on the "learn-by-doing" leveling system. I personally love the "learn-by-doing" system. I don't know what you mean by the x3 x5 thing, so I have no opinion regarding that portion of the learn-by-doing system in Oblivion. And as for the disparity in skills, well of course, if you didn't practice the said skills. I loved that part of the system as well. Of course, I haven't played the game again in over a year due to some glitch that causes doors to open slowly, so I've forgotten some things about it. What I do remember, is that I loved many of the ways Oblivion did things. I don't exactly remember any of the pet-peaves that I had about the game, although I do remember that there were some.
The reason I love the learn-by-doing system is because I am one that loves to get immersed into the virtual reality that I am playing. I love the learn-by-doing leveling system because it adds a level of reality that I very much appreciate and it does it's part in not reminding me that I'm playing a game. Not only that, but I found that the learning-by-doing system helped to change up the goals and play of my game. It gave me a reason and a goal to focus on with something like brewing potions or collecting herbs so that I can strengthen my alchemy skills. This was especially true with Oblivion where sometimes, after a while, it started to seem like every mission was just more of the same more or less, go get this or go kill that over in yonder place. Having that "learning-by-doing" helped to give me a purpose for taking my focus off of that for a while and focus on something different for a change. Also, I knew that every time I fell and got really hurt either by the falling or by constantly getting hit when I was almost out of health potions meant that it was all for the better in the long-term because every time that happened, I progressed towards being a little bit stronger due largely to the learning-by-doing system in Oblivion.
As for your opinion about the monsters and other enemies leveling up with you, I couldn't agree with you more. I'll tell you, if I ever designed an RPG game, it would be open-world, and I would set up a system of universal physics that applied to all characters realistically, (i.e. I wouldn't have animals arrested for biting/killing a person, but a hunting party might be sent after them) and to agree with you, there would be varying levels of enemies in different places, most designated, some not, all throughout the land. Some very high that you would have to wait until you were a high level to face, and some very low. Also, you'd have to be more careful, as in my game, you wouldn't be able to outrun a wolf. However, at the same time, I'd increase the character's awareness, probably through skills, of surroundings such as markings or tracks so that the player could be warned before running into a wolf. Although, the wolf may elect to run away if the player is not in it's territory, as most wolves prefer not to be seen by humans. I'd also increase the dynamics of sneaking and camouflage as hunters are often able to avoid wolves and bears altogether. (Likewise, in my game, enemies wouldn't always be on the routes between cities as those routes would be cleared every so often by the nearby cities. People would be able to report crimes and other issues, and the crimes would not be immediately reported upon being caught or seen. The knowledge of the crime could only travel from person to person, in other words people would not know about it unless somebody who knew actually got near enough to them to have conceivably told them.) My real wish is that people would come up with a game that just sets the basic rules of physics and law, and then allows the player to be as truly free as possible to be inventive, innovative, and resourceful about accomplishing missions or attaining personal goals such as building a little castle or creating a small militia to lead or inventing new potions with varying strengths. Oblivion did some of that with their spell creation and alchemy that allowed us to brew whatever ingredients we wanted to see what would happen.