A lot of games from publishers Happinet (all their 3ds games, so far had furigana) Furyu, Nippon Columbia, Rocket Company, Alchemist, Level5 games have furigana. Most games with furigana are fashion games like wagama girls mode (style savvy), aikatsu,himegal etc., tgc games, mondter strike, some rpg games like zelda, smt, pokemon, medarot, digimon (idk about latest 1 nr. 9 still trying to find out whether it has them ir not), simulation games like tomodachi life also have kana/furigana.
I'm also trying to learn Japanese, so I was looking into this. but gamelist so long if I post all names so I put dome publishers I saw vids etc. of that had furigana. Hope this helps a bit. Also I think the upcoming MH stories will have furigana.