These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
Mary Sue: Surprisingly, many of the important people described in the campaigns' scenarios tend to fit this trope. Partly justified however: most characters are supposed to have already lived several centuries, and to a certain extent you can choose the human you possess... So it's very easy to get carried over with the awesomeness of a certain character.
Misblamed: Nephilim is sometimes criticized for being a copy of The World of Darkness, but it was originally published in 1992, when Vampire: The Masquerade was less than a year old. Conversely, Mage: The Awakening is a rather obvious rip-off of Nephilim (backstory dating to Atlantis, five splats with elemental associations, grimoires used to focus spells, evil mages that have mangled their souls to become souleaters, etc.) and even shares some of the same writers, which may be the reason for the close similarity.
Unfortunate Implications: Chaosium planned to explore non-Western Nephilim in future sourcebooks, and kindly explained on its mailing list that foreign Nephilim would have fundamentally different elements, magic, and worldviews. No reason was given for this, it was explained as just being that way.
The French version explained that the non-Western Nephilim were exiles from Atlantis, and who used dramatically different rules to represent their cultural differences, even to the point of having different elements or not having metamorphoses.