I loved Lufia 2 as well, especially the Ancient Cave which blew my mind when I was younger since I didn't realize how they could make a full game and a replay-able 100 level dungeon in the same SNES cart.

My favorite game from SNES era is probably Tales of Phantasia though (the DeJap fan translation) - the gameplay mixed with a fun story across 2 different time periods was an amazing experience. I probably have FF5, 6, Chrono Trigger, Fire Emblem 4, or Star Ocean somewhere in the 2-6 range.

Lufia 2 came out in North America in May of 1996, just 4 months before the release of the Nintendo 64, so it may have been overshadowed. A lot of other late releases for the SNES are similarly underrated. Likewise with games like Kirby's Adventure for the NES, which was actually released 2 years after the SNES's debut!