About swapping armors between different foes: That could easily be taken away if you limited the amount of armor the PC can carry with him/her and even adding a system that takes time to swap your armor, meaning that if you get assaulted by a bear, you won't have time to change gear. And the percentage system that we had in Oblivion for example, didn't give us any good protection at all if we specialized in light armor and didn't have access to better types of material. A tiny 5 % protection was all that was given, it's neither realistic nor necessary to be bothered to use. The percentage system could be acceptable if they added some stuff suggested before, such as bleeding injuries, crippled limbs, injured limbs and locational damage. Each piece of armor would only protect the specific place they are at, thus meaning that a leather cuirass could, without being out of balance, with a light armor skill of 35 protect the chest up to 10%. It would also protect the limbs incredebully much compared to no armor at all from being injured or crippled and it would also protect the user from starting to bleed from every single hit to the chest. At the same time, the cuirass could absorb a small amount of some type of elemental damage, maybe up to 10% too.
All RPGs have very unrealistic inventory systems, because that makes looting more fun. There are popular and loved games that throw storytelling overboard and instead focus on looting and levelling. Players could potentially become upset if the PC can only carry a fraction of what they expect. Its much to risky to start messing with a system that players are used to and generally enjoys.
I don't see how a system that makes changing armor take time would be for the better. Is it fun to change armor before every fight? Does it add a feeling of realism? No, its a needless timesink and it breaks the immersion. An enemy should be beaten by skill and wit primarily, thats where the good gameplay is, good armor will increase the time one has and a good weapon will reduce the time it takes but neither should be a necessity.
Oblivion had very low protection values on some armors, yes, but that doesn't mean that the general approach is bad. I am also unsure how Oblivion handles a 5% damage reduction, if it rounds the damage down then 5% will always be at least one point of protection and that is pretty nice when foes hit softly like in the beginning, later in the game 5% will be moot. To have PC's with no armor get crippled by injuries pretty much only means penalizing pure magic users, as if their lower hitpoint pool and lack of armor isn't enough already. Lasting injuries could generally spice things up if done in moderation, just to make the PC appear to be bruised and in agony. But as soon as those become detrimental they may force the PC to take a boring trip to the nearest town to cure them, and that becomes an annoying hindrance if it happens three times per dungeon delve.
edit:
When it comes to armor and % damage reduction, its easy to be fooled by how the numbers work. The important thing isn't the actual % of protection, but rather the fraction of the damage that gets through. Its the fraction that has a significance on the time a PC can last in combat. Suppose a PC improves his armor with +5%, if he had 0% to begin with he will now take 95% of the damage and that increases his general survival time with 5.2%. On the other hand, if the PC already had 90% damage redcution the survival time will become doubled. Depending on the already existing armor, a flat +5% increase have very different impact.
A designer who thinks that this works linearly will make a flawed non-working armor system since he or she doesn't understand the consequences of any changes in armor values. Some understanding of math is required or it will end badly. The approach should not start with assigning protection values haphazardly, instead it should start with the question "how much extra survival time should this armor provide?" and then one calculates backwards and pick the damage reduction from there.
An armor that increase the survival time with 50% needs a damage reduction of 33%.
An armor that increase the survival time with 100% needs a damage reduction of 50%.
An armor that increase the survival time with 150% needs a damage reduction of 60%.
An armor that increase the survival time with 200% needs a damage reduction of 67%.