All the others I wouldn't describe as an RPG, but on Secret of Mana, Secret of Evermore, and the Ys titles have experience and stat gains over the other titles. Let's say that you remade Secret of Mana to play like Chrono Trigger and running into a Rabite would trigger the battle, what else is there that's different? The game includes rare item drops, gold to purchase a various amount of equipment that has to be upgraded, experience points to increase your stats and hp/mp levels, etc.
With Zelda, Illusion of Gaia, Evergrace, etc. What all these titles share in common are that they don't have any sort of experience gain. Health and sometimes power/defense up depending on the game, is found in secret locations and after defeating a boss.
Secret of Evermore and Mana take it one step further as there is the inclusion of the percentage on your attack rating. Attacking at less than 100% doesn't deal full damage, so in a way that sort of to counteract that it not being a turn based title. It still retains the I attack you, you attack me style gameplay, just this time you can dodge. You can't attack, attack, attack.