I tried to summarize what the production team wants and some other things. Remember that this information is from 2017 emails (most of it may have been changed), there are stuff that contradict each other because they come from different emails sent on different dates and information is missing because I didn’t have time to check all emails.
-Simple character designs (reminiscent of Star vs. the Forces of Evil, Gravity Falls, Mickey Mouse 2013, DuckTales 2017 and Be Cool Scooby-Doo), with fun and varied manestyles, eyes that are expressive and big (not overly big, due to the CGI from the movie) and a different body shape for each pony type. Earth ponies have large hooves, unicorns are relatively tall and pegasi have tiny wings in their hooves. Fur around hooves is something that most of the production staff disliked but shouldn’t should be taken off the table yet. Some potential design ideas to be considered may be big hoof feathers and a look inspired by the Gypsy Vanner breed for earth ponies, long horns, long manes, leonine tails and cloven hooves for unicorns and feathery, mohawk-ish manes (inspired by the Greeks), less hair and an aerodynamic look for pegasi.
-Applejack to be a tough, scrappy mare of short stature whose path certainly shouldn’t be crossed by. But she’s not cruel, she only has had a hard life since birth and has to work a little harder than everypony else. She probably won’t get along at all with Twilight Sparkle (akin to Sunset Shimmer and Tempest Shadow before their reformations kicked in) and may have a red streak in her blonde mane.
-Rarity and Fluttershy to have distinct horn patterns. (not sure about this one)
-Rainbow Dash and Pinkie Pie to have different wing designs from each other. Rainbow flies fast (like her G4 counterpart) while Pinkie will more likely flit around in a series of loops and hops. If most (all?) concept arts are any indication, Rainbow will have large wings while Pinkie will have small ones.
-The Mane 6 being in early adulthood, like in the current series, or perhaps in late adolescence (I didn’t understand that part very well).
-The existence of the Cutie Marks to be still fundamental, but no one in the staff apparently was fond of the current version (I’m extremely sure they’ll give a new meaning for them).
-Magic as something outlined, exclusive to personalities, visible in some way and not so common (otherwise, it would not be special). Visible and repeatable magic is/was the top priority for Hasbro’s superiors and the folks from Boulder Media.
-Ponyville being a colourful meadow (or at least more familiar and easy to relate than the others, to prevent places like a bakery and a school from looking and feeling out of place), Everfree Forest being an enchanted forest (obviously!) and Cloudsdale being a cloud town (once again, obviously!).
-The changes in Twilight, Fluttershy and Pinkie’s species were done thoughtfully, deliberately and for reasons that will be significant to all main characters’ personalities and the story.
-Non English-speaking markets have been pushing to have different translations of each pony’s name and Hasbro is willing to follow their suggestion. For example, Pinkie Pie would have a Slavic name in Slavic countries (Rozeta, Roza, Rozi, Rozovka…).
-Connected to the fact above, one of the people in production team suggested that some of the Mane 6’s names could be condensed in order to age-up the brand and make things less cheesy. For instance, Dash instead of Rainbow Dash, Pinkie instead of Pinkie Pie and Twilight instead of Twilight Sparkle. The other three would still be called as usual (well, it was suggested during the designing stage that Applejack would be nicknamed Apple or AJ, but they probably gave up on that idea). It was turned down because the character names are prominent, recognizable and, you know, trademarked.