What essential games am I missing?
Bravely Default. If you really like it then Bravely Second too. I haven't been able to get very far into the sequel before losing interest.
Shin Megami Tensei IV / Apocalypse, Devil Survivor 1 & 2, maybe Soul Hackers. Personally I think Soul Hackers has the best story but also the worst gameplay by far.
Persona Q. Etrian Odyssey dungeons with Persona III/IV characters.
Etrian Odyssey Untold 1 & 2, and IV. Maybe Mystery Dungeon if you like that style.
Stella Glow. It wasn't worth the $50 they wanted at release, but it's a solid game if you like SRPG grid style combat.
7th Dragon III. Currently playing this, so I'm not sure how it'll turn out.
I'd suggest 999, Virtue's Last Reward, and Zero Time Dilemma--and they'd be my #1 picks on the system by far--but you really should play the first two on PS4 or PC (in the Nonary Games collection) and ZTD on PC.
So I just acquired a 3DS to play Link Between Worlds (which I got with it). Currently it's on loan but I might buy it from the dude. He has it upgraded to 11.3. Can I roll it back? I've looked around and came up empty. I presume the hack isn't possible then.
No, once you update to 11.3 there's no going back and no way to jailbreak it yet.
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Atlus did their annual presentation a few days ago, and they're coming out with at least two more remasters of DS games (Radiant Historia and Strange Journey) and a sequel to Etrian Mystery Dungeon. All for 3DS, no mention of the Switch at all other than vague refences to SMT HD, and the working title for that combined with the fact that they are using Unreal Engine suggest that it probably isn't a Switch exclusive either.