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Come on, Toji had been in around 20 episodes by the time he was picked to be put in the Eva. He had the least development out of all the characters (apart from Hikari and Kensuke) but he was still a developed character. 
Also, when it comes to NGE's dark nature, it was laid out from the very beginning exactly what it was trying to be. It was Shinji being socially awkward, him confronting his father, being blackmailed to be put in the Eva and then the Eva having it's head blown through by an Angel. It set the genre and the tone, but of course it gets happier (with the same underlying themes) and darker. I can't be fully ambitious with what I'm trying to say, but it felt like the first episode of PMMM was trying to be one genre and the next it's a completely different one, which is disorienteering UNLESS there is an underlying theme or teaching in there.
For instance, if in the second episode Madoka goes outside and gets run over by a car, hospitalised and becomes paraplegic, the sudden change in genre and style could be explained through the theme of unluckiness and the morbid reality. However, the dramatic switch between a happy schoolgirl slice of life anime to one of the characters being eaten alive isn't justified at all (yet) so there's a definite clash of themes. At least in my opinion, that is.
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Sorry for forgetting about the synch ratio, it's put on now.