Since it's a separate universe and all, might I present the idea of Flash X Aria? I mean, Flash forgave Sunset and SciTwi, why not one of the Dazzlings? They can bond over music and Flash teaching her to play an instrument since she can't sing anymore.
Hm... well the first thing that came to my mind was 'well technically they never said Shining Armor and Cadence were together in the EQGverse so you can pair either one of those characters w/someone else and make more straight ship babies' but that probably was just my brain trying to make you draw one of my crackships so let's put that to the side for a moment...
Maybe Flash/Sonata, Gloriosa Daisy/Big Macintosh or Principal Cinch/Filthy Rich? Depends on what your Mane Six EQG ships are as well...
....oh no. now you have me shipping Big Mac/Gloriosa what have you done. Ironically, Gloriosa always reminded me of Cherry Jubilee hahaha. I do secretly kinda dig Cadence/Blueblood though, mayyyyybe I could play with that.
And the biggest thing is I don't really have any mane 6 EQG pairings //cries. I'm at a loss. teach me to crack ship and fall in love with them sempai
I AM PROUD OF BOTH OF THOSE THINGS. (please do think of the children. mostly me... ;D)
Okay so, allow me to try and help!
First of all, Mane Six x Mane Six - if you need any of those!
I'd say Raripie (if you don't want Rarijack if you do ignore this) they have a close relationship - the conflict with Rarity thinking Pinkie Pie didn't want her help in the first movie makes me think that they were close and it absolutely crushed her and meanwhile Pinkie didn't know why Rarity stopped talking to her and would try to reconnect but in Rarity's eyes it was basically her just keeping her on a string and she'd just get hurt all over again. As well Pinkie Pie's the one who always defends her costumes and those two get along very well in that movie and some of the short tie-ins. And they roomed together in Legend of Everfree so cute camp snuggles.
and Appleshy because with the new powers it would be pretty cute if Applejack and Fluttershy bonded because Fluttershy was able to talk to animals now and helped deal with critters on the farm.
Okay besides that, Mane Six pairings outside of the group:
Rainbow Dash and Sugarcoat - because Rainbow could use blunt honesty and it looks like Sugarcoat could use someone like Rainbow to loosen her up a bit - she'd be too harsh for someone like Fluttershy or Pinkie Pie but Rainbow could take it and give it back with the best of them and would force Sugarcoat to loosen up and be nicer bc of her loyalty to her friends - as well Rainbow could be one of the first friends she was really able to make on her own. I think once the matter in Friendship Games was settled she could try finding a friend and Rainbow instead of being turned away by her blunt nature finds it funny and it warms Sugarcoat up to her a bit because no one seemed to like how she was but Rainbow does.
Fluttershy and Photo Finish - could be cute, Photo Finish takes an interest in her and have an interest in her but not know how to handle it so she tries to make Fluttershy one of her models in Yearbook or something - at first Fluttershy is uncomfortable with it but through spending some time with her realizes that Photo Finish actually likes her and eventually the two come to an understanding and date - it makes Fluttershy more comfortable with attention bc her girlfriend gives her so much of it and she learns to like the art of what her work says even if it isn't her style to be photographed so much and Photo Finish tones down and kinda learns to respect her needs and as a result it makes her a much more sought after photographer bc she isn't terrifying her clients with her over the top personality.
Rarity and Flash Sentry - she always seemed to like Flash as a guy, thought his affections were sweet and he seems to be her type. Maybe there was even a point where they used to be friends and she liked him and Sunset in the past stole her chance as part of sabotaging Rarity's chance at Fall Formal Princess and of course Rarity was hurt but didn't dwell bc she's awesome except it really hurt to lose an old friend like that but as they spend more time together now those feelings kind of come back a bit. Not a lot just a bit. And when Sunset wants to just be his friend and the thing between him and Twilight is over, he kind of naturally spends more time with Rarity and realizes how much he missed his childhood friend and it slow burns for a bit until both really like each other but are unsure how to approach it but finally when they graduate she asks him to dinner and it becomes official and adorable. He dotes on her and she adores him - he makes music mixes for her shop and she dresses him for meetings with music executives and they become this really a-list pair in the future.
Pinkie Pie and Sonata - idk it's just cute to me bc of fanwork they can't all have these big stories...
Applejack and Adagio Dazzle - ... okay so Adagio's down on her luck and Applejack finds her like that, and at first Adagio lashes out at her but with a bit of trademark honesty and southern hospitality she's... not okay but at least willing to accept help. She's pragmatic if nothing else. Especially now. And so she becomes a helper on the farm. Pretty much everyone except Pinkie Pie (who's with Sonata) is against this at first, being that Adagio was a legitimately serious threat and unlike Sonata, Twilight, Sunset and Gloriosa she wasn't remorseful of her actions - however Sonata makes them realize that they were self-preserving. It doesn't make what they did okay and they did enjoy what they did but it was also what fed them and as an alpha female Adagio had to take care of her siblings and try to feed them. As well they spent a thousand years and more dealing with a lot of struggle and their time in Equestria wasn't as black and white as it may seem in stories. So she isn't heartless nor is she without the capability to adjust and feel remorse someday. Applejack is struck by this because Adagio providing for her siblings is how she is. Not the same obviously but as a girl with a sister she's do anything for she does get the need. And she sees Adagio has gone through a lot. So she tries to make her feel at home and it becomes a case where slowly they both grow to care for each other deeply. Adagio opens up to her about things that happen in her life and what immortality and the loss of magic feels like and Applejack sees her strength and is kinda ridiculously in love with her without realizing that. Meanwhile the kindness and honesty and home that AJ has given her has made her feel the same. Like, she didn't have many lovers in the past but she had some and damnit if AJ doesn't remind her of one. Plus she helps Adagio slow down and enjoy simplicity which is good bc Adagio doesn't know if she's even immortal any more and has to learn to cope with that possibility. Eventually they end up kissing during a very candid moonlight talk and become a couple. Maybe true love gives her her beautiful voice back but without the need to feed off of strife. Idk. Or not but the idea that suddenly she gets her voice back and AJ is nervous but happy to see someone she loves so happy but also lowkey has to try and bring up the whole 'hey so... you're not going to try that shit again are you?' without offending her new girlfriend.