As was already pointed out, yes, there are fixes that exist for issues in 3.5.
However, that ignores the point that there was a problem in the first place. Every one of your "misconceptions" Imaro are nothing of the sort. They really are problems that people have with the system. The fact that you can point to fixes for those problems means that those problems actually do, in fact, exist.
Yes, you can retrain. IF you happen to have a splatbook that came out several years after the release of 3.5. That still does not change the fact that you are stuck with bad skill choices by RAW. If you happen to incorporate the later patches, then, fine, that problem goes away.
But that in no way negates the fact that the problem exists in the first place.