this one.

and worse, they betray you, then they come back and everyone's happy!

also, beating a boss once (in a f***ng long battle), then after the battle you see that YOU'RE almost dying and the boss(es) is(are) alright. You beat them again and this time.. they die? OH MY! HELLO BATEN KAITOS, I'M TALKING TO YOU!

IMO the worst cliche in 3D jrpgs would have to be the excessive visual manga/anime style.
I'll try to explain.

Simple lush colourful 16-bit and 8-bit "character pixels" is very expressive and lively, unlike 3D character design. The gfxs used to be "so poor" that I had to imagine how the characters looked like. Everything was really immersive.
Nowadays, everytime I see the protagonist, I get so utterly disappointed. Most of us old school 2D jrpg fans who used to play jrpgs back in the 80s to mid 90s, resort to Western RPGs.

Occasionally I play the good old classics:
Secret of Mana, ActRaiser, Finaly Fantasy (Snes games) and Chrono Trigger etc..

Unfortunately the Golden Age of jrpgs is long gone. *sob sob*

@jordahn and Badgenome
they hit it right on the head!

I would add...
"..." too, every JRPG does it, it makes no sense. If you did not speak, why even put anything 0_O?

Heck, I compiled an entire list, ages ago.

http://www.skyrender.net/rpgcliche.txt

Though my all-time complaint for JPRGs in general is not on there: the extreme linearity of plot that inevitably permeates every single JRPG, even the ones that are ostensibly mission-based. I'm so sick of being railroaded in RPGs.

Comment on Suikoden IV...

SPOILER ALERT!!!

The main character's best friend (Snow) betrayed the main character.  Later, Snow was destituted and you could accept or not accept his return.  I accepted his return but refused to put the butt hole back in my party.  Got to the end of the game, but couldn't beat the final boss.  According to guides I read, it was strongly recommended to have Snow in the party so Snow and the main character could perform an effective "buddy attack."  I called bull on this one and decided to one day play through the game again with higher lever character at the final boss.  One day... One day...

Indeed. Save the ellipses!

The "..." doesn't bother me because it represent a sense of hesitation on the character's part since it seems hard to portray and represent that in a video game.

I was going to answer this post but my village was destroyed, just after I met with a child hood friend and I were discussing my amnesia and being an orphan. But I am sure my father wasnt some sort of legendary warrior or king.

silent protaganists!!!!! THis just needs to DIE!!!!

Only 2 games in history were ever allowed to get away with this.
Chrono Trigger: becuase it was so old it cannot be faulted for it.
and
Persona 4: because the game was just that damn awesome.

Yet even with these two, they could have been better with voice acting.

I've always though that Snowe was an excellent character, very well developed with his emotions very well explained. For me, he was the best character in the (rather mediocre) Suikoden IV cast