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Here are some stories I'd like to see:

If I recall correctly, Twilight's friends didn't see her meet Shiny and "Cadance" when she got to Canterlot. So they didn't know that she was happy when she heard Cadenza was Cadance, that Twilight knew Cadance as a kid, and Twilight only got upset again when "Cadance" didn't recognize her and treated her like crap. As far as they know, she was still mad for the same reasons she was at the picnic. I think the possibility of Cadance forgetting Twilight opens up interesting topics about "out of sight, out of mind" and how friendships can end or endure through physical separation. Especially since Rainbow Dash is getting closer to joining the Wonderbolts and all that. Also, RD and Pinkie Pie both have close relationships with kids they're not related to. They're sort of in the same position Cadance was when she was babysitting Twilight. I think the parallel of a similar relationship at different stages of life is really interesting and raises opportunities for introspection.

A crossover with another generation where someone freaks the hell out because immortal giant pony gods have appeared out of nowhere to govern ponies and the natural cycle of the world. Imagine if you woke up after being frozen in stasis for a thousand years, or slipped into an alternate universe, and found the United States was governed by an immortal monarch who was eight feel tall and had superpowers. And also they claimed to do some godlike task (like raising the sun) that, as far as you know, actually happens automatically. Doesn't that seem really sketchy?

Luna was so grumpy in the first part of the Crystal Empire episode because she wanted to go meet her fellow time-displaced ponies. As soon as Celestia's little test was done, she bailed for a while to go bond with them and hold seminars on adjusting to the modern era. "And this device, my friends, is called a toaster..."

After A Canterlot Wedding, Celestia is forced to undergo remedial combat training because just standing there shooting ancient Equestrian laser beams is a terrible strategy even when you're a nigh-invulnerable demigoddess.

Nightmare Moon wins. Several years later, everything in Equestria is dead from lack of sunlight, except for dragons, and she doesn't want those poopy losers as her subjects. She wants ponies. Thus, she resorts to conquering the sea ponies, whose ecosystem is mostly based off geothermal heat (is this actually how the ocean works? probably not!). Alternately you could write a Spike sadfic about him being able to survive on gems even after he's watched everyone he cares about starve and Equestria turn into a sterile wasteland, but why would you do that when you could write about those wacky seaponies unintentionally trolling poor Nightmare Moon?

For some reason, none of the "Luna adjusts to modern Equestria" stories have really addressed her relationship with Celestia to my satisfaction. Don't you think Celestia would have changed as a person after spending a thousand years ruling alone? Also, I really like the idea that even though Celestia was a loving and attentive sister, she was occasionally awful to Luna because she didn't understand when she was crossing the line between teasing or arguing and being truly hurtful. For example, using her own popularity to score points in arguments or bickering, or pulling the big sister card in situations when she should have been acknowledging Luna as her rightful equal. Stuff she would've stopped doing if Luna had explained it was hurtful, but that she shouldn't have been doing in the first place. So, with well-meaning-but-unintentionally-sometimes-horrible past Celestia in mind, I think it'd be funny to see Celestia spending the years 990-1000 frantically reading pop psychology and conflict resolution books and welcoming Luna back to Equestria with I-feel statements. Or possibly family counseling.