Some of these flaws are difficult or impossible to avoid. If you've spent the entire game building on your skill/stats/amour etc. and now you've simply become invincible, that is a design flaw. Why should challenge disappear as you approach the highest levels of experience? In the single player RPG's I grew up with, the challenge actually increased at the highest levels. In other words, you needed to be maxed out in your chosen skills in order to do end game content.
I think you missed the point. You keep presenting the acquisition of permanent invisibility as an inevitability: The fact is, this is a game where YOU DO WHAT YOU WANT, and if you think that just because you CAN do something means you HAVE TO, then you don't understand how an RPG works.
Let me present you with something of an anology: In real life, you can "break" life by disregarding women and entertainment and focusing on nothing but acquiring currency. As you get more, all of life's challenges disappear.
Do you understand the problem with that strategy? You CAN do that, but it's BORING. It is boring to become OP like that. Besides, who says that "winning" means "beating everything"? I thought winning meant "Being as happy as possible"? Well in an open-ended RPG, there's no "winning", there's HAVING FUN.
Some people have fun getting 100% invisibility. Others don't. Skyrim, just like Minecraft and Legos, is about doing what YOU think is fun. It's only as difficult as you want it to be.
So, let me ask you a question: if this is so bad, do you think the presence of a difficulty slider is a bad thing too, since on easy you can basically never die?