As with many of my General RPG rants, this is less an RPG problem than it is an issue of several entertainment mediums--hell, this problem's no less typical with anime and manga, and it's WAY more prevalent (and absurdly done, for that matter) in western comics. Still, RPGs do it plenty, and this is an RPG rant blog, so here it is.
Basically, there are too many goddamn resurrections going on in RPGs these days. I mean, it is getting seriously ridiculous at this point. In any given RPG, you're more likely than not to encounter at LEAST one method of bringing back the dead, which will inevitably be invoked at some point in the game to do just that.
You know, I remember back when death was considered to be, y'know, PERMANENT. When somebody died, they were supposed to actually be GONE. There wasn't some cheap, convenient magical stone to bring their soul back. There wasn't some techno-magic way to recreate them in their dad's basement. They didn't just have to wait until the next time they resurrected for no apparent reason to continue trying to take over the world. It used to be that defeating Death was the great, miraculous triumph of Jesus Christ, one of the most awe-inspiring moments of proof of God's limitless power and wonder. Now every character and his grandmother keeps half a dozen magic stones in their basement for quick resurrection jobs.
I don't mean, incidentally, items like the Final Fantasy Phoenix Downs, or Shin Megami Tensei games' Revival Beads/Gems/Orbs. In-battle resurrection doesn't really count to me, since most games, despite the names of their bring-back items implying actual return from death, simply regard going to 0 HP in battle (and, in a stupid few, 0 MP) to be a case of the character fainting, being stunned, or getting KO'd, to name a few game terms for it. If a character CAN be brought back to his/her/its feet during battle from 0 HP (in some games, like the Fallout series, 0 HP really is just plain death with no remedy), it's very rarely referred to as death. So when I talk about cheap resurrections, I mostly mean ones that occur via plot.
Now, it's not that it's ALWAYS cheap and empty in RPGs, mind. I can think of a few moments where I don't mind it. Chrono Trigger, for one--the journey to take Crono back from the grasp of death is one that involves great struggle, the great knowledge of not one, but two insanely wise sages, and winds up bending the laws of the universe to go back in and then FREEZE time--an action that's not even so much resurrection as it is causing the death not to happen in the first place. Then there's Shadow Hearts 2, which resurrects Alice using the knowledge of Roger, who is a scholar-of-all-trades who's lived for centuries, and a book of forbidden knowledge of unknown origins--for a moment. But then the process goes wrong, and fizzles out, and Alice dissolves back into nothingness--because defeating Death simply can't be done by mere mortals, even with all the knowledge and science in the world on their side.* The games hammer home the fact that bringing someone back from the dead is actually a BIG DEAL, instead of just coming up with one excuse after another involving Farplanes and Lifestreams and other such magical plot contrivances to bring back a lame villain half a dozen times.
And of course, there are a couple of times where it's been an integral part of an extremely well-devised plot that I won't complain about. The resurrection of the characters in Shin Megami Tensei 1 is acceptable to me, given that the game is an insanely brilliant analysis and commentary on Christianity and thus the resurrection helps to draw necessary parallels with Jesus Christ that are fun to mentally chew on and dissect. And the implied reincarnation of the cast of Shin Megami Tensei: Digital Devil Saga 2 also is quite acceptable, given that the game is based on, analyzes, and comments on the theology and philosophy of Hinduism and Buddhism, of which reincarnation is a very integral part. These are cases where death being temporary is a necessary component for a highly intellectual and fascinating plot. It's not just another typical case of, "Well, we know we killed this guy, but we really liked him, so let's bring him back just because!"
But overall, seriously, enough of this. Enough of the Dragon Balls, the villains that just grow back like crab grass, the dead characters coming back to life at the end of the game for no adequately explored reason, and so on. I may be happy to see a character I like get a second chance, but it just overall cheapens their original death scene, and begs the question of why they'd be killed off to begin with if the writers couldn't take not having them around to complete the story--a question that can almost always be answered, "Because we wanted a quick and easy emotional scene, and couldn't be bothered to come up with anything but the cheapest, most typical way to get it." Why have a villain die if dying isn't going to cease his machinations at all? Doesn't that defeat the entire purpose of killing him? Death should have consequences. It should mean permanent loss of life for the characters and all the emotional hardships that go along with that for the people who mourn them...and it should also mean permanent loss of that character for the writers. It shouldn't be a thing the writers flip like a switch. If they want to use a character's death to enhance the telling of their story, then the writers should be prepared for the downside that the character is gone. Because when they don't, the entire thing just starts to lose all meaning.
* This good idea and lesson is, of course, totally disregarded and crapped on by Shadow Hearts 3 later saying "lol n00b ur doin it wrong" to Roger, and has some random middle-aged bozo complete the resurrection process. But if the only good parts of SH2 that you counted for anything were ones that SH3 didn't ruin, you'd practically have to disregard the whole game.