For gameplay-focused JRPGs (my favorite type of RPG), there are some mechanics that come up near-universally in the genre (and many appear in RPGs that don't fit this distinction; a fair number are very common in party-based RPGs regardless of other characteristics) that I happen to dislike.
* Dead characters receive no XP. This is especially annoying (in games where bosses give XP) if this happens at the very end of the boss fight. (Random note: When I was playing Dragon Quest IX (one of the rare few RPGs to not have this issue, though it has others of its own), my main character was dead at the end of the final battle. She got XP (enough to level up, as it turns out, but you need to be alive to actually gain the level), and because she was important to the ending, the game revived her with 1 hit point. Hence, my clear save had a main character ready to gain a level, but who still had to fight a battle (any will do, as long as she survives) to actually level up.)
* Death cures everything. This is something that has never made much sense; if a character dies and is revived, all effects on the character are removed. (This actually makes it sometimes worth it to kill a character on purpose. It also has been the cause of an exploitable glitch in at least one game; in Baldur's Gate 2, if a character dies after casting Shapechange, the character permanently gets the spells's benefit.)
* Permanent missable items. I do not like missing something because I choose to proceed with the main story rather than exploring. To me, a player shouldn't be penalized just because she prefers to do things in a different order.
* Missable stats. This applies to any game where level ups are finite (in other words, there is some level cap, even if it's rather high) and where level ups either are random or can be influenced by some factor, and where there isn't an alternate way to make up for this. Final Fantasy 6 and 9 are offenders here; your stat gains at level up are affected by equipped espers (in FF6) or equipment (in FF9) at the time of level up. This isn't an issue if infinite stat boost items can be obtained (like in FF8 or Dragon Quest 3), or if you can always create new characters and there are no "special" characters. This is also why I prefer FF5's system to Final Fantasy Tactics's system.
* Unskippable cutscenes, of course.
Darvond: Forced stealth, especially if it's the kind that kicks you back to an arbitrary point instead of letting you fight or run.
This is actually a dealbreaker for me. Unless there is a way to skip the sequence or trivialize its difficulty, I will not play the game, and I will not buy the game if I hear about the sequence before hand.
Also, I thought of another:
* Skill point systems without easy respec. The problem here is that these force permanent decisions on the player, and making the decisions permanent discourages experimentation (experimentation being something I find fun) and can lead to a player being stuck due to have made bad decisions (or decisions that happen to suffer from balance issues making them unexpectedly bad)l.
