Yes, as per the defitions of "Hero", "Hero Card", "Hero Character Card", and "Hero Target" in the Enhanced Edition glossary, hero character cards are not hero cards and are not part of hero decks. It is true that the definition of a "Character Card", which I had not noticed until dypaca pointed it out suggests that hero character cards are hero cards, which seems to contradict the wording of the previous 4 definitions.
dypaca, as for your other questions, hero targets would still include hero character cards even if they are not hero cards because the definition of a hero target is "any target that is also a hero card or a hero character card. If a card affects non-hero targets, it can affect any targets that are not hero cards or hero character cards". The defintions of "Villain", "Villain Card", "Villain Characer Card", and "Villain Target" follow the pattern of their hero counterparts, which would mean that non-hero cards would include villain cards (but not villain character cards) and environment cards, so no, the character cards would not be shut down by Ground Pound, for example.
Thematically, Isolated Hero makes no sense at all, because if the hero were truly isolated from the rest of the fight, either that hero or all of the other heros would also be isolated from the villain. It's hard to imagine a situation in which the heros are completely isolated from each other, but are in no way isolated from any of the same villains or environment features.
Everything I've found in the rules so far, with the notable exception of the defition of "Character Card", as pointed out by dypaca, suggests that character cards are not part of decks. Aside from everything I've already pointed out, there is also the fact that in the Enhanced Edition component list, it separately lists 10 hero character cards and 400 hero cards, and then goes on to say that each hero deck contains 40 cards. If you look at spiff's card list pdf (http://www.spiffworld.com/sotm/files/sotm_card_info.pdf), you can count the cards in the hero decks as 40 and see that they don't include hero character cards.
phantaskippy, I have not ordered a replacement deck, but a hero is not playable without both a hero character card and a hero deck, so it would be nice for hero character cards to be included with the replacement deck orders. That doesn't necessarily mean that the hero character card is part of a hero deck in gameplay terms, however... it could simply be included as a "bonus".
dypaca, if you believe I'm trying to twist the rules to a certain outcome, then you have the wrong impression of me. I'm simply trying to resolve cognitive dissonance so that I can be confident that I'm playing the game correctly, and I don't particularly care which interpretation turns out to be correct, so long as I can have confidence in it. The bulk of the evidence supports the interpretation that I'm arguing for, but I agree that it's not clearly correct, which is why I'm hoping to see some official clarification that resolves the contradictory wordings in the rules.