Aw hell, this is a really tough question. Between Secret of Mana, Chrono Trigger, Xenogears, Grandia II and Shadow Hearts: Covenant it's really hard to decide.
As for mechanics I wish were more wide spread, though- the Wild Arms mechanics of allowing you to evade random encounters if you don't feel like fighting them by expending recoverable points and an automatic gauge that heals your HP at the end of combat until it runs out at things I think should be in more games (or at least the ones which refuse to give up on random encounters). The Force Point system is also brilliant, but that's a bit too specific to the series.
As for mechanics I wish were more wide spread, though- the Wild Arms mechanics of allowing you to evade random encounters if you don't feel like fighting them by expending recoverable points and an automatic gauge that heals your HP at the end of combat until it runs out at things I think should be in more games (or at least the ones which refuse to give up on random encounters). The Force Point system is also brilliant, but that's a bit too specific to the series.