Well, depends on the system honestly. For NDS, the only true hidden gem is the original 7th Dragon which is a great game despite being one of the hardest games of all time (to the point people had to mod-in a super easy mode because the "Normal" difficulty for it was about 15 times harder than any of the old Etrian Odysseys' "hard" difficulty just to give you a reference). For GBA, Serious Sam was a nice Doom clone, the Summon Night games were just super interesting at least for the most part, the old Fire Emblem games such as Sword of Seals (from back when the series was actually good and especially that third one that was Japan-only), Batman Vengeance (port of the PC game but someone much more fun to play than original), the Mother 1+2 dual game cartridge and Mother 3 (I mean, of course, not hidden, but hardly anyone plays the GBA version despite being the superior one), Samurai Deeper Kyo (based on that really easily forgotten classic amazing anime and is a fun top down slash and hack), pretty much ALL Yu-Gi-Oh! games besides that Duel Academy one and that will do for now because there are close to 100 games I could recommend out of the ~18000 titles the system had. For older games I'll just suggest Yu-Gi-Oh! Dark Duel Stories (I loved this game since it allowed you to create your very own monster cards, which was fun) on the GBC and Mario Picross (the father of all other picross games and possibly the hardest and most punishing one) also on the GBC. If you want recommendations for a specific system besides those, just let me knowany hidden gems I should know about?
and yeah pretty stupid, because this just is asking for it. I mean what else would you expect