No one asked Yui if she even wanted this
With the new RP-first system, I used SYNC to send messages to relevant authorities. As it's a collaborative body with no new personnel being hired for it, it was assumed that Yui wouldn't care, given it's internal organisation between already standing forces and corps. Nothing "new" is being made, in fact it's supposed to trim the bloat, which should help with forum RP by removing complexity. It makes one body to contact for mission support, rather than 5, 6, 7, 8.
Wasn't Feyani the guy Yui pulled from Director of MP job and stuck him at a base so she didn't have to work with him anymore?
Feyani is the Director of SARA. She has bright ideas about reforming things - this would be her third reformation. IIRC, Yui just had a disagreement about some of those efforts with the MP. I know you don't like seeing MP in plots because you think it's stifling, so if I recall the IC reason for that was Yui stepping in and removing some of the changes, then transferring Feyani. A lot of those changes in MP still remain, however, and she had excellent ideas for SARA, so I don't imagine it was a big scandal outside of Yui not liking certain parts.
Players choose if their character or plot is "elite" or not
I don't think this affects the playerbase nearly as much as you imagine - we already have existing special forces on most postings. There's SAINT and its flavours, SOFT, Giretsu, Rangers etc. As I've stated several times through the wiki article, special forces aren't "better" than regular soldiers. Rangers, for example, are worse than regular Infantry at things like line-fighting, which is the most useful skill on plotships. "Elite" is a word I don't see applying to these forces in most cases, "Specialist" would suit better - like a Technician, or a Medic. I don't see the spotlight being taken from anyone. If anything, special forces will be less popular in those sorts of mixed plotships, because the scenarios they are good in won't come up as often as scenarios that Infantry would be good in, but when they do it'll add flavour. Honestly, SAINT is a much bigger culprit of the 'elitism' problem with their black ships and gatekeeping of equipment - has been for years. Hopefully that's changing soon.
Regular ships like mine might not get the cool missions anymore
None of this should affect plotships, given that GMs control that - I don't see why this would detract missions from plotships. Proximity and practicality are often more important than getting the perfect team in any case. The niche missions are already mostly done by special forces in the wider sector, because the forces that specialise in those already exist, such as SAINT, SOFT, etc. This is just a reorganisation, all the roles already exist. Again, SAINT has been the problem with 'taking the good missions' for many years. If anything, this should help regular plotships, because GMs can quite easily engage with SASO to get support if players drop out mid-scenario, they can get crew special training JPs prior to difficult missions. They can also have spec-ops mission scenarios delegated to them from this single body in the absence of local, better suited forces, and are therefore more likely to earn their secret ops medals, capture medals etc.
You're going to have new players join, immediately roll special forces characters, and then play their characters in a way that makes no sense for someone with years of elite training
Again, this isn't adding new roles really - just rolling together those ones that exist on the wiki as well as those that would in practice. Honestly, I think people being able to do such things as make Officers on character creation makes this pale in comparison. Officers have to give orders to other players, directly affecting their RP choices - special forces will be doing their own thing with the other enlisted forces when on mixed plotships. The same issue you're stating already arises with people playing scientists and engineers in any case. I get what you're saying, but it's easier to play a special forces dude than a scientist with 2 PhDs. Again, those special forces dude roles already exist, this article doesn't change that.
I don't want Star Army Special Logistics to work for SOCOM
No problem. It just seemed like SASL was an orphaned body which was a mix of SAINT codeword clearance and Logistics bureaucracy and looked like it needed a home.
TANTO identities are not listed as being known by the Director of Star Army Personnel but I feel there's no realistic way for them not to be
Correct me if I'm wrong, but current SOFT teams already only report directly to Star Army Command, bypassing Personnel Command - at least this is implied looking at the Command wiki page. I don't mind adding Hanako in too.
I'm worried about creating another division of Star Army that I will need to run or staff for HR/sustainment reasons at a time I'm especially worried about staffing the Star Army with played characters.
This should trim more than it adds in practice, which helps simplify the process of RPing with a number of different corps. In fact, it adds no new command positions. All members of the command unit are already the commanders of their individual forces. It should cut down parts of monoliths like SAINT that are unwieldy to NPC. It also centralises a lot of that problem with many different divisions - just send a request to SASO and they'll disseminate it out.