Though I'm not a Rioter, I have responses to your points.
- Over the past months, Riot has clearly intoned that they want champions to have niche points and areas. They want both definable strengths and definable weaknesses. After having played her new style kit, she actually reminds me quite a bit of Karma (new style), in the constant AoE capabilities that she brings. Previous Sona did have stronger "fire and forget" poke, and new has less "fire and forget" with some forced interaction to keep the damage equal. Case in point, Karma inhabits the "long range poke and long range utility", whereas Sona inhabits the "shorter range poke and utility". I understand the difference is not appreciated to some, but it's enforcing variety in a game where sameness can kill.
On a personal note, I have been able to successfully play her with the heavy harass style of old. The numbers have changed, but the playstyle is still available.
As for the ult "scaling" her other abilities, it's to incentivize people getting E prior to level 13. The base numbers are strong enough to be workable/strong at the relevant levels, but the upwards scaling with ult ranks always you to neglect a skill yet still have it get more before you can properly attend to it with points. I, personally, feel it's elegantly done and feels very nice. To a degree, they could remove any of the extra shield/speed/damage and I would still be more than able to make Sona work very well. Perhaps if they nerf her, that's a good place to examine.
- As for the 100/150/200 mana cost of the ult, I question that decision as well. They've been normalizing at 100 for ult ranks for a while now, and I don't see an overarching reason why hers is different.
I'm assuming you're talking about the "one of the big reason people bring Sona to a game, is the power of her ult", and why you might feel the rest of her is tuned low to "balance that power". First thing's first, Sona's ult is different from Nami's ult. Nami's has quite a bit of range, but aside the small annoyance of the knockup, you only really inflict a slow... Also, the ult is quite avoidable range/kit depending.
The different between a slow and a stun... is seeing a LeBlanc distortion in and catching her before she can pop back away from your team to safety. The life saving halt to a Fizz that just dropped from his pole onto your AD carry before he gets his full rotation off. The immediate shut down of a surprise lane gank that was stupidly grouped against a Sona.
You might argue that Nami brings her bubble stun, and it isn't an ult. You'd be right. However, it's smaller and considered hard to land. Arguments vary. Nonetheless, Sona can damage reduce a diver or team of divers and stop them dead. Nami can briefly buffet that, and slow them... and depending on player awareness/skill, stun them after.
- I've read several of your back and forth discussions with Fearless, and he repeatedly apologizes for what he thinks was a lack of interaction of his part. I've read him apologizing enough times now that I genuinely feel concerned that he may take this whole situation as a strong negative experience and back away from what he does. I think the end result is quite a bit more fleshed out and realized than prior Sona (and I recognize our differences of opinion), so for my part... I hope he keeps with it.
Please recognize that Fearless is just a dude going to work and doing a job. If he were a talented chef hired by Burger King to figure out a different way to cook the Whopper, he may well catch hell from thousands or millions of hamburger eaters country-wide. Still though, he's just a guy going in to work. He works on a game for a living. You don't know if he's a hugely outgoing person in his social life. He might be great at bouncing ideas off people, but be very focused and run solo when doing the hard numbers. He says he read though the hundreds of pages of Sona comments, critiques, ideas, and feedback? I believe him. I also believe that's he's just a normal dude, going to work...