It's a shame to hear that Tokyo Ghoul went so downhill after the first season. I thought the first season had some great ideas and some excellent episodes (namely the first few episodes and the final episode) but even that season had a middle portion that's just kind of a hazy memory to me at this point.
From what I understand (I might be wrong on this) the manga itself had some confused priorities regarding its tone, pacing, genre and plot structure, and it seems that confusion has been carried over tenfold into the adaptions. And switching back and forth between anime only and closely following the manga just sounds like a headache, like if they wrote FMA Brotherhood like it supposed to be a part of the same continuity as the original FMA adaption.
You have my respect for attempting to cover this madness. I feel the most sorry for the fans though, I'm sure there's a lot of great material to uncover if one has the patience.
If one has the patience, and if one has the funds. Manga is a pretty expensive hobby, when you compare it to the cost of watching an anime. Which makes it even more unfortunate when the creators of an anime cut out information assuming that you have first invested a considerable amount of time and money into other areas of the franchise.
Ideally, you should be able to watch a series or movie without feeling like the only way to "enjoy" it would be to skip it entirely and view it in another medium instead. That kind of just defeats the purpose. At that point, why make an anime at all? You could just make another advertisement for the manga. Unless that's actually all they ever intended the anime to be...a really, really expensive advertisement for the manga.
I feel like the process of adaption has become so commonplace in the anime industry that I'm fairly sure these anime are just made on reflex, 'because that's how it's done'. Like creating an anime adaption is what lends legitimacy to the manga, Light Novel, or game property. As if the property doesn't have merit or isn't 'popular' unless it has an anime, which doesn't make all that much sense if you really think about it. Maybe the producers see anime as just a high-budget advertisement, but I have to wonder if the animators/directors and writers and such could really tell you what the purpose of one of these animes is. As far as I know, the original Mangaka or author isn't really directly involved with these projects, so they're always working with somebody else's work rather than producing something that came fully formed from their own imaginations (though I'm sure plenty of them are fans of the properties they work on.) I'm probably wrong about this since I have no insider knowledge, all we can do is speculate really.
It feels like adaption in anime is about trying to blow through plot points as efficiently as possible rather than trying to take advantage of the strengths of the medium, which is somewhat of a shame, really, even if that's not their intention. Adaptions do work sometimes, though, if only because of law of averages... one has to work eventually.