The story Togo is telling when Yuna is stuck in a coma is actually the exact story of what Yuna is undergoing at that exact moment. The moment after the battle where her fairy doesn't appear nor does she get any flower petals like the others makes it clear that she is different from the others, and the moment where she goes dizzy at the end is actually a subtle clue that Yuna is still fighting alone with no one else's knowledge.
In Episode 7 Fu half-jokingly asks if they can eat the offerings at their resort room, claiming that it's okay to take back offerings after they'd already served their purpose. This is the leading theory as to why the girls recover from the effects of the Sange in Episode 12; the girls had already fulfilled their duty as Heroes, and so the Shinju didn't need their offerings anymore.
Speaking of Fu, when it comes to the Sange she seems to get off rather easily compared to the other girls, only losing a single eye and later one ear. But as the Cool Big Sis and leader of the group, seeing the other girls suffer worse disabilities (especially Itsuki, whose loss of voice drastically affects her social and academic life and her dream of becoming a singer) affect her much more than her own problems.
Why exactly do the Shinju need young girls as sacrifices? Sure, there's historical precedent, but that's not a reason in and of itself. But notice that the Vertex are specifically sent by other gods with a mission of purification. Maybe that's why they have to be fought with pure, innocent young girls and flower petals.
Yuki Yuna's confrontation with Togo, insisting that she'll always remember and that everything will work out all right: at first it seems a bit flat, as she really doesn't have any evidence to back up her position, and cites only her feelings. But what if you take this flatness of this argument at face value? It's perfect. Yuna really is arguing a position with nothing but her feelings to back it up, denying all evidence to the contrary. In a very real sense, the fate of the world is hanging on by this thread - on Yuna's blind faith and her hope that everything will turn out okay - and for all intents and purposes, she's wrong. And Togo believes in her friend anyway. (This Fridge Brilliance might just also double as Fridge Horror.)
If you actually think about the different losses that the girls face after their first times that they go Mankai, they all seem very disheartening effects for the characters in their personal life. However, if you look at it as though the shinju tree wanted to keep them capable of continuing to fight, it all makes perfect sense. In fact, it almost seems as though the tree MUST give them a disability and choices the most tactical disabilities for each girl in particular.
Yuki loses her ability to taste, which is awful for a girl that desperately loves food and comments the most about the taste of the food she eats. However, by giving her this disability, the tree prevents her from having any severe limitations to battle at all. This is important because although Yuki isn't the 'leader', she is the one with the most battle prowess.
Mimori loses her ability to hear, which for a girl who already can't walk is shown taking special care to listening to music, even more than the future singer in the group. However, as a sniper, not being able to hear might actually be a minor blessing as it will allow fewer distractions to affect her shooting. Also, it is important to note that Mimori is the tactician of the group, and is generally giving hints to take down the Vertex, not receiving hints.
Interestingly, this also extends to when Mimori was Sumi Washio. The first thing Sumi lost was her ability to walk, which was because the new Hero terminal traded in her bow for a sniper rifle. She wouldn't need to be running around like she used to since the gun requires the user to remain stationed and have precise aim. Now the next thing the Shinju took was her memories up to that point. It may seem strange that the Shinju decided to take one of their two heroes out of commission, but remember that everything after the events of Wa Su Yu was set up by the Taisha. Sumi lost her memories so that she could befriend Yuki Yuna and become a hero again without knowing about the Mankai system. Sonoko was powerful enough that she could take out the army of Vertexes on her own (at a heavy cost), so the Shinju decided to keep Sumi active so that she could join another team.
Fu loses her ability to see in one eye, and while this girl is generally the first to enjoy beauty (check the bridge scene in episode 1, she is clearly enamored) now she is limited to seeing it in only one eye. Think about it though, out of all of the girls, which one would have to deal with sight the least in battle. The sniper would clearly need her eyes, the pugilist would need to see attacks from the side, and the girl who has (essentially) a string trap weapon would need to see three dimensional layouts of the forest. The only one who would not need both eyes is the swordswoman, whose sword can literally change sizes as she sees (no pun intended) fit. She has the weapon with the least amount of optical necessity.
Itsuki loses her ability to talk, or vocalize at all. This is, of course, a very powerful blow to the team, as the Itsuki had finally decided to start singing in a professional sense. There is an entire 3 episode arc of the anime that deals with this loss, as it is considered the most unfair outcome of the lost senses/abilities. However, if you were to rewatch the show, and look at all of the times that Itsuki talks during the battle scenes, you would be at a loss to find anything of major importance (not counting exclamations of surprise or pain). In other words, she barely ever talked on the battle field in a way that would be helpful to the other girls, or that helped the battle end quicker/better.
It might be important to note that although the tree might not have had the ability to directly affect the lost abilities/senses, it would appear as though the Mankai 'curse' only affects the girls in a way that will not prevent them from fighting.
It seems strange that Yuna, Fu, and Itsuki's hairs become toned to their theme colors when they transform but Mimori and Karin's hairs only slightly change. That's because Mimori and Karin have the first hero terminals that were upgraded with the Mankai system, with Mimori's terminal from her time as Sumi and Karin's being originally owned by Gin. This is further evidenced by Sonoko who has her terminal upgraded the same time as Sumi's and also has her hair become slightly darker rather than have a purple hue.
This also explains why Mimori and Sonoko's Mankai takes the form of giant warships with giant forms of their weapons attached to them instead of rings on their backs, as they had the first version of the terminals with the Mankai upgrade. Also Yuna, Itsuki, and Fuu's terminals were created after the events of Wa Su Yu, and although Karin did inherit Gin's terminal, it wasn't upgraded at the same time Sonoko and Mimori's were, and was intended to be used once the new hero team needed support.
Sonoko is noticeably missing most of her limbs. Sange only causes you to lose the ability to use certain things, not physically removes them. Her amputatons are probably related to health issues related to whatever else she lost.
The BDs revealed that this was just a case of Off-Model; the corrected version clearly shows that she still has her physical limbs attached.
Karin went Mankai in the final episode despite being partially paralyzed and blind deaf. What could she have lost if they had not been cured?
Despite the after effects of Sange, imagine Mankai and Fairies never implemented for Hero System. Even if Sumi and Sonoko somehow repelled the last attack of Vertexes, second and third generation of heroes had to fight for their deaths, Togou would remain as Sumi and never try to destroy barrier, thus never leading events of Shinju trusting humans enough to sacrifice himself. So heroes would never have their Earn Your Happy Ending and humanity would be destroyed completely
Aki-sensei's final fate. She essentially betrayed both her former students and left the Sentinels and humanity in general to die in the hopes of gaining instrumentality only to fail at the end. And as the Sole Survivor of Taisha she will have the bad luck of getting stuck with the blame of the conspiracy by default. Even if the Hero club forgives her the adults will most likely not. And the Sentinels who already hate Aki-sensei's guts would gleefully lay down vigilante justice on her especially Mebuki who would not miss an opportunity for a Civil War scenario with Karin. Aki-sensei will be forced to spend the rest of her days in hiding hoping that she won't get caught by people seeking revenge, former students wanting payback now that Taisha has crumbled, or even friends and family of Gin who can now engage in Best Served Cold without Taisha's protection.
Speaking of the Taisha what about the ones who gained instrumentality? They are now basically an abandoned wheat field in the middle of nowhere as far as the world knows outside of the Hero club and Aki-sensei. And unless by some sick ironic joke this is how Utano's dream of replanting the world once the vertex are gone is achieved. They are now essentially at the mercy of nature or some random guy who decides to harvest some perfectly good wheat just lying there not knowing its people. It's unlikely anyone in the hero club outside Yuuna would care to show mercy to basically learn how to take care of a field. And Aki-sensei has enough problems on her plate dealing with the fall of the Taisha.
Sonoko regenerated her limbs somehow. This has left fans wondering if it was originally an an animation error, there's an in-series reason for it, or if the writers decided to retcon her being paraplegic as it was either too dark or they decided to change the outcome of the anime to be more positive.
Sonoko only appears once in the final episode. Togo got her memories back but doesn't seem to care about her former best buddy.
It's implied that Tougou's the person Sonoko is talking to in the bonus chapter of Washio Sumi, which takes place during and after Episodes 9-12. Sonoko After confirms this and confirms Togo's memories returning, showing that Togo and Sonoko have restored their old friendship.