Okay:
Character 1: Bosmer, major skills are stealth oriented
Character 2: Orc, major skills are combat oriented
By level 30-40 it doesn't really matter what I started in, the character will be good at everything. Despite the orc being much larger in size, the bosmer will be just as strong and do just as much damage in melee combat. The orc will be just as spring-footed and sneaky as the elf despite being way bigger and clumsier. 100 strength for a bosmer should mean less than 100 strength for an orc, despite "capping" the skill, the orc is a lot bigger and therefore should always be stronger, an orc at 100 strength should be stronger than a bosmer at 100 strength. A bosmer at 100 speed and agility should be faster and more agile than an orc at 100 speed and agility because they are smaller and quicker.
With fallout, you're generally playing one race, which is human, but you define your strengths and weaknesses through the fixed attribute system, so at 8 strength, somebody will be a lot stronger than somebody at four strength, but the person at four strength will be better at something else.
I dont really see that as a flaw, or a problem. In fact I dont really mind it at all. I dont want to be penalized for picking a certain race.
It kind of sounds like that is more of an issue of races and their associated skills and attributes and so on, rather than leveling issues. You say that a level 100 strength orc should be stronger than a 100 strength elf, but that doesnt really have any relevance to the issue here in my opinion. The only way for that to make sense would be for the orc to have a 'bonus' to strength. It doesnt really apply to a problem with the leveling system. At the peak levels (50 or more for Skyrim), of course all of your attributes will start to beef up, even the ones you dont really use as much. Personally I like this, because it gives me a chance to switch the game up a little. I like doing a little bit of everything.
And as for other characters, enemies, creatures and NPC's......not EVERY thing in the game has to be level based. There should be certain people and places that you should avoid until your a weathered, well leveled character. They shouldnt be easier just because Im level 1 when I get there. Guards should be a high level at all times, as well as other NPCs and even animals. I certainly dont want deer getting stronger as I level....and there should always be people smarter/stronger than you, but the balancing factor is the skills.
Someone in TES might be a better fighter than me, but I have potions, magic, great weapons and armor, and extremely tailored skills that I can use to take them down. Thats what can give me the upper hand in a fight against someone stronger.