I'm not convinced that turn-based gameplay has been "perfected." If anything there hasn't been enough variation on the 1986 Dragon Quest formula. ("Let's make it an action adventure." isn't improving gameplay, it's scrapping strategy for something more accepted.)
RPGs are strategy games and like board games, which weren't perfected a thousand years ago with Backgammon, they're not going to expand as long as they stick too close to Dragon Quest, Wizardry, Ultima, and D&D. RPGs, quite frankly, haven't quite reached their Monopoly, Guess Who, Ticket to Ride, and Scrabble days yet.
JRPGs have barely expanded on the facets that set them apart from Dragon Quest. Going back a great number of years, many of the games have strategic elements that were glossed over once, then barely expanded on while everyone else copied them.
(1987) Final Fantasy 1 has your characters stuck in their commands. In other words, if an enemy or ally dies, your character will still try to attack or heal them. Thus, strategic foresight was a necessity.
(1987) Megami Tensei had monster catching, fusing, and an Auto system.
(the monster system was then adopted by Pokemon which was adopted by.. everyone?)
(1991) Final Fantasy IV had the Active Time Battle system which (unlike a speed stat) made it possible for enemies to interrupt strategies randomly, leaving room for error. This left room for complex strategy in battle as the system could have easily evolved this as new enemy actions get introduced. Instead, the system eventually evolved into Final Fantasy XIII's... which Square still seems to be trying to "perfect"..
(1992) Lunar: The Silver Star had distance penalties (where character placement was an active issue)
(1992) Shining Force allowed you to recruit a massive number of characters, all with unique abilities and equipment. You could swap them in and out via a central base. It and Fire Emblem's gameplay are the basis of nearly all Japanese "tactics" games.
(1993) Secret of Mana had weapons and magic actively level up as used.
(1994) Earthbound (Mother 2) had odometer health, requiring the player to think ahead a before deciding whether to continue the offensive.
(1994) Final Fantasy VI had desperation attacks and equip-able magic-teaching mediums.
(1995) Chrono Trigger had combo attacks
(1995) Lufia II featured interactive environments and puzzles rather than empty corridors of chests and monsters. Also featured an "Anger Gauge" that allowed you to use the special powers equipment if you took enough damage. The result was magic gauge whose spells were unique to nearly every weapon and armor you could equip.
(1996) Madou Monogatari: Hanamaru Daiyouchienji removes the health bar, enemies send the character flying, and the character's facial expression determines her status.
(1997) Final Fantasy VII allowed you to customize your skills by combining them with modifiers.
(1998) Panzer Dragoon Saga...
(2002) Xenosaga has environmental features that you could activate that effect the enemy before you fight them.
(2003) Shin Megami Tensei: Nocturne has the "press turn system" where criticals, weaknesses, dodging, blocking, and reflecting have massive penalties. It also features Magatama, which give your character strengths & weaknesses when equipped in exchange for skills when you level up.
(2008) Valkyria Chronicles introduces turn-based strategy to a HIGHLY hostile real-time environment.
(2012) Final Fantasy XIII-2 has... semi-interactive cinematic gameplay
I'm pretty sure turn-based strategy games are just starting to see innovation.
Maybe the generation of developers that remembers the days of Wizardry, D&D, and Dragon Quest are finally retiring.
