I have a question. Do you guys think the reason why Kakashi neglected Sakura was because she resembles Rin? By putting her out of harm's way, Kakashi wanted to protect her and prevent the same history happening again.
No.
I think it is author neglect. Nobody (in series) complains, references it, or otherwise acknowledged it happened. Consequently, it's hard to give any hidden meaning to it, especially as it relates to Rin. That is the effective result, but I think the author was trying to do or suggest anyhing by it.
Naruto had an opponent who nearly killed Hinata. Sasuke had an opponent who outright tried to murder Lee (and whom releasing all those Gates did minimal damage). Sakura did not. From Kishimoto's stand point, it's probably that simple.
Kakashi did foist Naruto onto Ebisu, and this is a violation of showing and not telling. Ebisu was stated (and by implication) to be good at what he did. He was a poor match for Naruto and Kakashi deserves criticism for not following up on this. However, Kishimoto gave Ebisu butt-monkey treatement, so readers didn't take him seriously and it comes off worse Kakashi than was probably intended.
Moreover, Sakura is equally at fault. You say it's not a good excuse? You're right, it's not, but you act it as it relives her of the duty to better herself. When Naruto didn't get training, he asked for it. When he was unhappy with what Kakashi gave him he ultimately found his own.
Sakura eventually does this, but not during the chuunin exams. If she is unhappy with where she stand at what point does some of the burden fall on her to do something about it? If anything, they both deserve blame for that. I fact, when she does become unhappy about the gap between her and her teammates she, to her credit, does something about it. But nothing stopped her from doing that before.
-Even though she was the first one to complete the tree climbing, he didn't teach her anything more while the boys were training.
Doesn't he have her helping out with the actual mission while they are left behind in the forest (when they would both rather be helping with the mission)? It wasn't a training trip. It was a mission.
-He gave Naruto and Sasuke the duty to fight against Haku, while Sakura had to protect Tazuna (basically just standing there and reflecting any projectiles)
So?
You realize the problem with this argument right? It means whoever gets assigned to guard Tazuna is being neglected. So is the only way to not do that is send them all to fight Haku and hope no one gets past their opponent and offs him?
Which time? If it was the last, I recall Naruto jumping into that one all on his own rather than being assigned to do anything.
-In the Chuunin Exams, he taught Sasuke, dispatched Ebisu for Naruto, but basically didn't give a thought for Sakura.
He didn't think of Naruto either. Naruto went to him.
Moreover, Sasuke was fighting Gaara. Lee used 6 gates and still didn't do any real damage and even though he was clearly out of it by then Gaara tried to murder him anyway. Moreover, Sasuke was a marked man by another Sociopath.
He should have set something up for Sakura and Naruto (without prompting), but I can kind of understand why Sasuke was the focus here.
-Kakashi saw Sakura's power-up only after the three-year time skip. Didn't he meet/train with her even once?
You tell me. Kishimoto has ret-conned from this time period before (Kamui), so I don't think you can assume anything. Moreover, she is recieving personal trainging from the Hokage. If I'm him, I'd check up on her sure, but I'd stay out of it unless otherwise asked by the student or the Hokage. But, how do you know he didn't check up on her?
-When Sakura and Naruto was talking to Kakashi that they have failed to bring back Sasuke and that he has become too strong, Kakashi told them that he thought of a very effective training. Then he said that the training is only for Naruto. He didn't think of an effective training for Sakura?
Was she unhappy about it? It's the same thing as before. To the extent it's neglect, I am more inclined to hurl the accusation at the author, because so much of the neglect accusation is by implication. Otherwise, either nobody notices or nobody cares they are being neglected because nobody ever mentions it except for Naruto and Ebisu.
The series never attempts to answer whether he a good teacher or not, so I am relunctant to read much into what you say when nobody in the series seems to give a crap. That apparent apathy tells me that he is not trying to infer neglect at all. And this is especially true of Rin. I can't imagine that the neglect shown through implication is the result of a motiviation that doesn't even get that much of a nod.
And if the series even does try to say he's a good one, then you get a pretty decent example of the difference between showing and telling.
So, no, I don't think they are at all related until such time as the author demonstrates that and the neglect accusation is better reserved for the author than the character.
2.) It was said a few chapters ago that team 7 was back. But when it comes to the most important part such as stopping Obito or bringing down the Bijuu, it's not team 7 anymore. It's team Naruto + Sasuke. If team 7 has indeed returned, Sakura should take a part of it instead of standing on top of Katsuyu and being an observer (like she always does). She's basically looking at their backs letting them do the fighting. Chapter 632, "this time we're going back to back" has just disappeared somewhere.
It's not nearly as bad as Team Not Seven, but she seems to suffer from the same problem they do: the author is having trouble finding a consistent role for her in the primary plot. That shouldn't happen with your heroine.