SNES
1) Final Fantasy 6 - Probably the best of the era. It has a good story which is decently told in the story half of the game, and the end of the world feeling in the second half works as you try to rally hope once more. End with a decently strong finish, and you get this placement.
2) Chrono Trigger - Plays a lot like FF6, though with a fluffier story and characters that makes it more of a popcorn game. And I tend to grade a well done serious game higher than a well done fluff game simply because it's harder to pull off the former well.
3) Phantasy Star 4 - A serious tone all around, without the same degree of customization the top two contenders had. Sadly, the same game where they got the Phantasy Star system to finally work, and got everything working was also the last game. But, if you have to go, what a way to go.
4) Final Fantasy 5 - A bit of a drop here. FF5 is passable in plot and character, and relies entirely on gameplay. Good thing it's pretty decent in that regard. Nothing too special, but a fun diversion regardless.
5) Seiken Densetsu 3 - The beginning of the average titles. Again, a best of series nod in a game that's somewhat fun, if not fun enough to grind through it three times to see all the plots. Especially the random way you have to get your third class.
6) Final Fantasy 4 - This is... sad. FF4 is, as far as I'm concerned, the worst core FF. Granted, it's a fairly good series, so this isn't saying too much, but it still shouldn't be halfway up the list. Ah well... bad battle system, a plot that is basically a rehash of a previous game that doesn't manage to be clearly better, and no real strong points.
7) Breath of Fire 1 - I don't know why it is, but there's only two BoF games I like all that much. The menu system for the most part feels too stiff and tends to turn me off them. And the first game definatly has this as its greatest flaw. Aside from that, pretty good for its era, and a plot that was able to entice me to finish it.
8) Shining Force 2 - The game that wanted to be Fire Emblem. I don't mean the series, I mean the game that started the series and lacking the polished added to its descendants. Better than the original, but that's not a high accomplishment.
9) Breath of Fire 2 - See BoF1, but take away interesting plot with one that takes forever to show up, and is practically unintelligable through bad translation.
10) Secret of Mana - It's like SD3, but worse in every way. Which I suppose is to be expected in a series. That said, I have always been fond of the opening.
11) Ogre Battle - I've tried to like this game, just... it's too slow paced. Combined with getting vindictively punishing near the end after an already overly long game.
12) Earthbound - Somewhat quirky, the humour needs you to be in the right mindset, with the right tastes, in order to enjoy a game with nothing else going for it. And, even if you do have all that, the humour dies out around halfway through, leaving you with nothing but a horrible shell of a game, and a need to beat it only to justify the time you've already spent to get that far.
13) Tales of Phantasia - I'm not a big fan of this style of combat. Add in a seemingly pointless third arc after what felt like the right time to end the game and you get a low score.
14) Super Mario RPG - See Earthbound except not adding additional fail at the end, just less awesomeness. Now, this isn't the sort of humour I'm inclined towards, and I like the controls even less.
15) Lufia 2 - The most generic game in existance. Possibly the worst game, in the worst series, and hence, bottom of the list!
PSX Era, 1
1) Final Fantasy Tactics - Possibly best game ever? Could be. Either way, solid battle system and excellent story, and the remake doesn't hurt this.
2) Final Fantasy 7 - Good story that, oddly for an RPG, doesn't spell everything out like you need your hand held. Battle system needs a lot of work, and Squenix is holding too fast to this world, but otherwise a very solid game.
3) Breath of Fire 4 - One of the two BoFs I like. Battle system is good, menus don't clog everything down, and it's generally fun to play.
4) Brigandine - So high up because this is the sort of game I like. Of course, the last two thirds of the game are a highly boring slog because no one on the map can touch you any more. But it's good until you take down your first opponent.
5) Suikoden 1 - A nice solid game that doesn't fail anywhere except polish. Honestly, a remake with good production values would be a sweet little game.
6) Vagrant Story - I'm never going to replay this, but I really did enjoy the one playthrough of this game I did do. Just really fun with good presentation.
7) Final Fantasy 8 - I'll admit, I'm a lot more forgiving of this game than most folks are. I just like it more than it's objective worth suggests it should be liked. That said, this just means it's the best of the FF Trio of Fail, though a good jump ahead of the other two.
8) Lunar: Eternal Blue Complete - Oddly missing something that it's predecessor had. Not entirely sure what, but it's not quite there. That said, it's a solid sequel, and therefore deserving of a middling spot here.
9) Legend of Dragoon - A competant game with a plot that is befuddling and gameplay that's fairly easy so long as you don't screw up the timing. Of course, if you ever put the game down for any length of time, good luck just picking up where you left off.
10) Chrono Cross - This game is the evil opposite of Chrono Trigger. Where Chrono Trigger was good, this game is bad. Notably, exchanging a light fluffy and oddly coherant plot with the most serious, angst filled, incomprehensable dramafest this side of Fanfiction.net, as well as preferring a large cast of one quirk meat puppets over a small cast of adoringly detailed cliches. That said, if you can ignore the plot (denial: it's not just a river in Egypt!) all of its parts tend to be better together for something reasonably fun.
11) Star Ocean 2 - A mostly generic world is saved by mostly generic characters in a battle system that's not all that good.
12) Wild ARMs 2 - Incomprehensible plot backed up by Bablefish on the translation duties? How can this fail!
13) Dragon Warrior 7 - Back in the day this was grouped in with Xenogears and Suikoden 3 as the games that are too damned long. Of course, unlike those two, this game didn't feel like it needed more fleshing out. No... it needed either a complete repurposing, or a bloody good editor. As an anthology of stories, it could have worked. Of course, then you'd need gameplay worth having, and not tying everything to the same grinding system that hasn't been in vogue since the NES games. Of course, since the battle system is effectively unchanged since the NES days, it's not like it really matters. At least it looks like a SNES game.
14) Persona 1 - Why is this below Dragon Warrior 7? Because even though DW7 is an overly long piece of tripe, it's at least playable. I tried to play this, really I did. But the stiffness of the menus, conversations, and, well... movement, just made this unplayable. No comments on battle as I didn't get that far.
PS2 Era, 1
1) Wild ARMs 4 - The plot is solid, and the gameplay is fun, but the real star here is the character interaction. Sure, they're not all deep or angsty, but they bounce off each other great. And it feels nice and refreshing to have a character whose not only full of youthful optimism, but youthful optimism that doesn't make me want to bash his head in with a shovel!
2) Suikoden 3 - Honestly, battle system is too stiff and animations take too long. That's the only real flaw I've found in this game. Well... that, and I seem to have developed a pathological hatred of the Northern Cavern, but that's neither here nor there. Otherwise, a top notch game that isn't quite as good as WA4.
3) Grandia 3 - I haven't gotten to the point where the plot fails utterly yet. It's just failing normally. That said, I've always loved the idea of the Grandia ATB system, and hated the fact that, well... it wasn't needed. The fact that it's not only needed here, but emphasized makes me a happy Canuck.
4) Kingdom Hearts - It's light fluff that you don't need to think about too hard. Generally enjoyable with some definite style points.
5) Xenosaga 1 - The characters at their best, some neat NPCs/villains, and nothing too overblown yet, along with a nice simple battle system. Sadly, the high point of the series.
6) Front Mission 4 - Only half-way through. Not entirely sure why I stopped playing, but I did. But I do intend to play this again sometime, and it may move then.
7) Wild ARMs 3 - I tried to play this, but I find it... well... the gameplay feels lackluster to me, along with the rest of it. It is pretty, and the plot is enjoyable. Just, playing feels more a chore than anything else.
8) Tales of Symphonia - A few neat ideas in the plot, followed by your traditional get the eight MacGuffins and Tales battle system. Over all, not that notable.
9) Valkyrie Profile 2 - A system where what you need to do well is determined mostly by random drops? Getting rid of the simplicity and uniqueness of cast that made it's predecessor so good in order to make a game populated by souless clones? A story that seems to be the height of 'Why?' And not the CC "What were the writers thinking" why, but a more general why is anyone doing any of this why.
10) Xenosaga 2 - Yay pretentiousness! Yay complex and tediously slow battle system. Yay world filled with witless idiots that can't do a single bloody thing for themselves! Yay hiding the cool bits behind a necessity to get a specific item early on! The only good thing about this game is Alpedo, with bonus points for the fact that he took it upon himself to answer a question immeadiatly after I asked it to the Elf.