Mother 3 is right behind it though. Although I didn't play the previous two games in the series, the combo system in M3 makes me like it better anyway. And storywise, I would say it's better than anything in the Pokemon series. It's probably the best story in a game that I've played, period.
I was waiting for someone to mention this game! This is DEFINITELY my favourite RPG ever--in fact it's my favourite overall video game. Yes, it even beats Chrono Trigger and Final Fantasy VI, which are both very good, don't get me wrong. Why? Well, it's mostly because the battle system. There's just something about turn meters I don't like, and the Square games are rampant with them. It kinda pressures me to hurry up in making battle decisions, which I don't like at all. Especially since it takes time to scroll through the techniques in Chrono Trigger, and to figure out all the complex battle options of FF6.
Mother 3, on the other hand, is practically flawless in my opinion. Okay, the only negative it might have is that its graphics are not fantastic, and it has this weird glitch where the music speeds up on the menu screens. But the gameplay is very smooth, and there was no point in the game where I was confused on what to do, unlike in many RPG's and Zelda games (which, by the way, are NOT RPG's--they're in the Action Adventure genre for the most part) that are out there. I really like straightforward plots, which this game definitely has. And it's not a boring plot either. Like Sydian said, it has a wonderful storyline. And some really interesting characters that actually have backstories. I really love the chapter system: the story is broken up into eight chapters, some with different characters, and one that is from the enemy's viewpoint.
Another thing I really like about Mother 3 is how much that game has improved as a sequel to Earthbound. There are lots of mechanistic things I can complain about in Earthbound: counter-intuitive controls (pressing L to talk to someone?!), healing being complicated and costing money, difficult-to-cure status problems, disgusting enemies (I'm looking at you, Master Belch), no easy way to run/dash, key items taking up space in the inventory, etc. They fixed ALL of that in Mother 3. Every single one of those things. And added some neat features like a Battle Memory (a Pokedex of sorts for enemies) and a sound test feature as well, and of course the battle combos that involve the tempo of the music. Without any loss of quality from the more appealing aspects of Earthbound either (except a more compact overworld). The characters and enemies were both more interesting, healing is MUCH easier... I could go on.
In fact, the improvement thing can also apply to Pokemon Black/White as well, easily my favourite Pokemon game so far (I have yet to play the sequel). I LOVE how they gave those games a much better storyline than the previous games (which were quite lackluster in my opinion). N is actually a really interesting character for once. I like how the rivals are more than petty jerks, and how there are two of them. I like how they improved on mechanistic annoyances like TM's being used only once, the low-health beep being turned into a music piece, and poison not causing damage while walking. And as with Mother 3, they greatly improved on the music as well. Though Heart Gold and Soul Silver had some really good music too.
I haven't really played a lot of the 3D RPG's, so I can't really say much about them yet. I'm really looking forward to playing Persona 3, Eternal Sonata, and one of the Kingdom Hearts games, as soon as I get the right consoles (I only have Nintendo consoles).
