What about a good game with good implementation where every element implemented was carefully considered by someone who is very passionate about the project and is a talented game designer?
For a good game, this is usually the case. But I think your unstated assumption is that this "someone" is/should be one individual. For smaller games, maybe. For larger games, this is impractical.
There is nothing wrong with tinkering with a formula when it is necessary, but every step away from the original idea is likely going to detract somewhat from its personality. Of course it can improve the end product but it seems obvious that starting out with an idea that needs a minimal amount of tinkering and having said tinkering done by the person who originally came up with the idea will result in a game with more soul.
It depends. The "soul" and "personality" include how open to collaboration you are, how you handle other people's creative inputs and willing to compromise when you might be wrong or misguided. A game designed by a tyrannical dictator may certainly have a strong soul, and you probably would feel it through the end product.
This is a very idealistic view of game design, I just think that there is nothing wrong with the ideal itself. And that it could be strived for a bit more in the gaming industry, especially the indie community.
Perhaps. I don't think it is the most pressing game design problem in the game industry, indie or not.