It's an odd idea. Falling in love with a pony who's literally you (just as the opposite gender). Just the thought would be plain weird. They'll literally you in almost every aspect, but there was an... connection that the Mane Six couldn't resist about their counterparts.
It all started on the day Twilight and Dusk Shine, her male counterpart, discovered each other's world. It was a great shock at first, seeing what they look like as the opposite gender, but a time went on, it seems kind of normal in a way. It's a little freaky though.
As for the 'connection', since they are technically the same pony in a way, they have a similar thought process.
If Rarity thought about making a white dress with purple gems, then Elusive thought about making a white vest with purple gems. If Pinkie thought about throwing a party with blue balloons, then Bubble Berry thought about throwing a party with blue balloons. You get the idea.
Since they have a similar thought process, they easily know what they want.
Others may say if they always know what they're thinking, then wouldn't it be 'boring'? In some ways, it it, but at the same time, it's kind of sweet in a way too. Being able to know what they like.
Isn't it narcissistic? Since they literally look like each other with a few different design elements. Yes and no. They may look like each other, but at the same time, it was oddly comforting, seeing something familiar and yet different, like how Dusk's mane and tail is more 'choppy' than Twilight's straight locks.
This 'connection' isn't completely romantic either. After some surveillance, the Cutie Mark Crusaders didn't act all that 'lovey-dovey' with their male counterparts. They were more like friends, almost like siblings. While there are some hints it might grow into more when they get older, like Silver Bell pulling out a seat for Sweetie Belle or Scooteroll being a little defensive with Scootaloo when any other colt notices her, but those are simply speculations since it could be just simply being nice or having some sibling defensiveness and it would be proven when they're in their teens or so.
As for the interactions with ponies who've already been paired up before all of this, they were simply friends too. Shinning Armor and Cadance enjoys Gleaming Shield's and Crescendo's company, even if there are two alicorn babies to take care of, while Big Mac and Sugar Belle kind of like the idea of having double dates with their counterparts coming along. From what Pinkie told Twilight, Maud and Mudbriar are really happy to have ponies who have their interests.
Most of these interactions were positive. The few negative interactions were usually with ponies who don't see their own flaws. For example, Spoiled Rich couldn't stand being in the same room with her male counterpart, saying how incredibly rude he is.
Still, maybe it was the 'comfort' that made the ponies of Equestia to accept their counterparts easily. A sense of comfort, companionship, acceptance, etc. This 'comfort' is what makes them either fall in love or be friends with their counterparts. An almost unbreakable bond.
Maybe it was for the better that they've met each other, seeing how almost every pony here in Equestria was happy in some way.
AN: Yup, this fanfic is what I'm going to end the Mane Six pairing project. A selfcest fanfic. Hopefully, you enjoy it, though I admit it's not all that romantic (and way shorter than I thought). It's more like a... theory(?) on what would happen if Equestria just so happens to find out they have opposite gender counterparts and were able to meet them. Sorry that it's nothing too special. Also, don't worry. This isn't going to be the last fanfic I'll make on this fandom.