I have to say, Kishi's trolling has become so bad that it is literally destroying all the integrity of his once great manga. I'll try to focus on the ones I feel that Kishi handled the worst. Feel free to discuss and add your own.
1. Kishi has created so much circumstantial evidence that Tobi is Obito that he literally has destroyed his own reputation as a story writer. There are so many facts that can prove in an instant that Tobi is not Obito that it is truly a joke, and Kishi even hinting at the prospect is degrading to himself.
He has obviously set up that Tobi has Obito's eyes, but I don't think he's quite set up that Tobi is Obito. He could go with something like the story in starwars, that when Obito got crushed by the rock, the good part of Obito "died" and the new evil Tobi was "born", and that therefore he but that seems like a stretch. I think by saying
2. It has been confirmed that whoever Tobi is, he is using Obito's other sharingan. Not only that, but it is established that he absolutely has to be using Obito's MS in order to be accessing the other dimension. This means that Tobi has had, and has been using, MS this entire time. This, by far, is one of the biggest trolls you can ever hope to even imagine. This basically means he is constantly using MS in battle without overexerting himself with chakra use. It also means that his MS design might be the same as Kakashi's, unless the design is unique to the person it spawns in.
Yeah, this is a big problem. First, when we do see Tobi's eye, it's clearly in regular sharingan mode and isn't showing an MS pattern. Second, since we know that MS techniques drain a huge amount of chakra AND cause you to go blind, there are two options:
1) Tobi has found some sort of way to use MS-alike techniques with a sharingan without actually having to unlock/use the MS transformation (and do so in a way that doesn't require a huge amount of chakra) or
2) Tobi has EMS, and therefore has much larger chakra reserves than normal, is immune from blindness, and is able to use his techniques like Sasuke and Madara use their MS techniques without draining all his chakra.
Of course, if Tobi has EMS, we certainly haven't seen that and we definitely don't know who he would have gotten the other eye from (Obito's father? Some unnamed brother?)
One good point is that this would explain why Kakashi uses his MS eye without going blind. Maybe Obito's eyes are just immune from blindness? But that doesn't explain how he's able to use the space/time techniques so much without running out of chakra? Maybe it's Hashirama DNA magic?
4. Despite sending himself to another dimension to escape damage, we have never once since Tobi's body parts go out of sight. I guess you could say that we don't see them disappear since something is always overlapping them, but the way the last 300 chapters have gone, the visual interpretation we get from the manga is that Tobi's body still exists in the material world even when he's transparent. Kishi now saying that those parts of his body aren't actually there when he phases through is a serious troll.
Yeah, it is a little bit weird. So are those parts of him that are in the other dimension still "connected"? Do the parts in the other dimension have access to his chakra network still? Do the parts in the other dimension have blood flow? Is that why he can only stay intangible for 5 minutes at the most, since it's like holding his breath and his parts will die if they stay away for too long?
Sasuke and Karin have spent some time in that other dimension. Have they seen parts of Tobi's body just randomly appearing and disappearing there? Fuu and Torune were there too. Did they ever try to attack those floating bits to see what would happen? Wait a minute, how did Fuu and Torune get their arms tied behind their backs, that's not what they looked like when they got absorbed? (Chapter 520).
If Naruto allows himself to get absorbed, will he be able to hit the floaty parts when he's in that other dimension, even though nobody else ever tried it?
5. Gedo Mazo has been going critical for at least 5 or 6 chapters now.... and still nothing. Kishi has gotten so sick of drawing the Gedo while its freaking out that he has pretended its not even there anymore. Not only has the gedo been going critical for 5+ chapters, but the army of allies have been running to Naruto's location for abut 30-40 chapters and haven't gotten there when it only took 2-3 chapters previously for them to move the same distance. Not only that, but we haven't seen the Madara/ Kage and Oro/ Sasuke plot lines in a number of chapters despite them seeming to demand instant attention.
Stop trying to make sense. Time doesn't work the way you would expect it to.
6. The way Kakashi has been using Kumai, HE SHOULD BE LONG DEAD!! IDC how much training Kakashi has done, the way Kishi established Kaskashi's ckakra threshold and his limits at his age, he should not be able to use Kumai as much as he had considering his past problems with it. Not only that, but Kishi is obviously planning for Kakashi to use kumai perhaps 5 or 6 more times before he lands substantial enough blows to actually defeat Tobi. This is another very significant troll, and more of a plot hole really, that Kishi is abusing to the fullest.
I've mentioned this elsewhere, I'll mention it here again: It's possible for Naruto or Killer Bee to give Kakashi more chakra to use his technique with. Also, we know that Kakashi is able to open at least one of the 8 gates. He may also be familiar with things like food pills or other chakra enhancers. I'm only saying it's possible.
I could go on about Oro being sealed and yet being revived through one of a thousand curse seals.... or Madara knowing the secret seals that can override Edo Tensei despite the fact that not a single user of Edo Tensei seemed to know it.... but you all know these are serious stretches on the plot of Kishi's part and trolling at its best.
1) That does fit with Orochimaru's repertoire of snake techniques: All of his techniques seem to show that his "real" body is really a collection of smaller snake pieces, and most of his techniques involve using multiple smaller snakes from his body. Splitting himself up into many smaller bits is just part of who he is. Don't think about it too hard.
2) Madara was a founding member of Konoha and, for a time, a close ally of the senju. It's very possible that he knew some of the secrets of Edo Tensei from Tobirama himself. Tobirama, when he was summoned, was always under Orochimaru's close mind control and was never able to break out. Madara was only able to do it himself in the brief moment between the time the technique ended and the time when he would have disappeared. Tobirama never had that chance, because Orochimaru never released the technique. Again, I'm not saying it's a good explanation, but Kishi can weasel out of this one if he wants to.
2a) Also, keep in mind that Orochimaru is a bad guy and had a bad-guy version of Edo Tensei. From what we know of Tobirama, he was a good guy and probably had a good-guy version of edo tensei. Tobirama may have only been summoning friends and allies, and would have given them the tools to break out of the contract. Again, it's all speculation but we have to assume that Tobirama's version was different from the versions used by Orochimaru and Kabuto. Orochimaru and Kabuto wouldn't have allowed their slaves to break out, but Tobirama might have been nicer.
You bring up a lot of good points. Some parts of the manga really do seem like Kishi is making things up as he goes, and he hasn't had a real plan in mind for the last few years. This means that certain old facts sort of need to be ignored and new things have to be jammed together to fit the direction he wants to go. I hope he pulls things together a little bit more tightly, but it's hard to see how he will be able to make sense of everything.