Megas

Having read the premise as well... it basically did just sound akin to a prototypical version of Dragon Dropped  (although we would've at least been spared from the obnoxious meme faces of the latter episode) - I concur that the episode we received, while clunky in multiple ways, was an improvement (personally, I've never fully disliked SaYS in itself - it's a heavily flawed episode (particularly regarding Spike's characterization), yet the M6 themselves are well-characterized and resultantly receive some memorable comedic moments (Dash's fanfiction and the reactions to the rock tower in particular are golden)). As for the writers' preference towards Rarity, I suspect that their more stringent quality control towards her episodes (at least within the context of the show's initial crew) stemmed from her relatively subversive nature for a show of FiM's demographic in the early 2010s - prior to FiM, the majority of 'feminine' fashionista characters within girls' media tended to be shallow, unlikable archetypes, whereas Rarity is presented in a far stronger, more dignified and well-rounded way (at least once the crew finally determined how to use her character effectively circa Suited for Success) and I believe the crew themselves may have recognized (and acknowledged via their more 'regulated' treatment of her character premise-wise) this bucking of convention as a result. 

Speaking of which, you may have also uncovered Merriwether William's dropped outline for a musical episode involving Twilight temporarily assuming Mayor Mare's place (the leaks actually indicate multiple episodes (including one planned for season 6 where, bizarrely, she rigged a general election to enable Discord to become the mayor of Ponyville, which ultimately leads him to plunge Equestria into eternal darkness... because someone asked for it) were planned for MM, all of which were canned early in production), with its rejection presumably explaining why she was reassigned to write SaYS's script - while the outline itself does contain some overly cheesy/obvious elements, it arguably would have enabled S3 to more effectively build towards placing Twilight in a permanent leadership capacity (and highlights the 'leadership qualities' Celestia claims her to have developed in MMC). 

I wish Rarity had an episode in Season 3. I wonder why she didn't. 

In regards to the Rarity thing, I could actually buy that for the first half of the show. The second half though just felt like Haber was playing favorites. He regularly considered Rarity his favorite and it really shows in both his writing and story editing(notably how he handled a good chunk of her focus episodes)

And yeah, I read that synopsis with Mayor Mare, it sounded really interesting and I honestly wish it could have happened, given it could have given her more characterization as well as be an early start for Twilight becoming a leader. I guess they could never get it to work. The one with Discord sounded awful though so I'm glad that one never happened

I'm guessing they were never able to get one working right, she was the only one to have multiple ideas for one while the others had just one set in stone(Apple Family Reunion and Wonderbolts Academy being good examples). Heck, before Sleepless In Ponyville, the Luna dreamwalking episode was originally planned for Rarity and Luna, and there was one for The Crystal Empire starring Twilight and Rarity