I love 2 things, programming and telling stories. Since high school I always wanted to be a game developer. However, overtime I realize something, I dream to big! From the start, I always imagined that my games would be massive 3D games. It's when I sat down and realized a few things, that's when it really came into perspective. I'm not good at art, so creating 3D environments is not an option. However, I know someone who is willing to give her time to make 2d characters/environments. Which brings me to my next question. Do you know any 2D games that have good game play, BUT also a good story?
Some of the older RPGs for the SNES had amazing stories and gameplay. Chrono Trigger is probably my favorite. The older Zelda games were really good, too. Man, I'm getting nostalgic just thinking about all this.
The old Lucas arts graphical adventures spring to mind. Especially Secret of Monkey Island and Day of the Tentacle.
Metroid Fusion is my favorite of the sidescrolling Metroids. Going through my steam library I'd say Cthulhu Saves the World, Rogue Legacy (not a great story but an interesting idea), Home, They Bleed Pixels, and debatably Starbound. None of these are particularly story-driven, barring maybe CSTW since it's an rpg, but personally I think games that give the player just enough to inspire them to make their own stories are some of the coolest (see Starbound).
Chrono Trigger, FF6, FF4, Fallout 1-2, Earthbound, Mother 3 and those would be my main suggestions. Not sure if Grim Fandango counts or not but I'd reccomend that as well.
As an indy dev myself, I suggest you think hard about the type of game you're making too. What genre are you thinking about? If you naturally gravitate toward 3d games, my guess is that you like 3d action games (fps, unchartered, GTA -- most AAA games these days). Think about what mechanics are best suited for 2d games. Would you be interested in visual novels? What about turn-based games?
I played this game on Steam recently called The Cat Lady. It's a 2D game that's mostly puzzles and problem-solving. It has some really dark themes and sometimes graphic imagery, but I really enjoyed the story. I definitely recommend it. I've never played anything quite like it before.
Cave Story. Hell, "story" is even in the name. Also, it is free, so you have no excuse for not downloading it right now and playing it.
Golden Sun for sure! Two games each about 30 hours with tons of great world building and an interconnected narrative. Characters are well written as well.
I totally second Final Fantasy VI (which has one of the best villains ever), Chrono Trigger, and Metroid Fusion. I'd also add Super Metroid to the list: It has very little verbal story-telling, but it has one of the most epic endings in any game ever without a single word spoken. It's a masterpiece of gameplay, game design, and stands out as a surprisingly strong example of non-verbal storytelling. It also has an atmosphere/ambiance few games can rival even today, so you can learn a lot about how to create a specific atmosphere (in this case focusing on isolation and solitude in a dark sci-fi setting) just by using the right kind of music, level design, and even color schemes. The majority of the most recognisable pieces brought back from the original Metroid for the NES were composed and arranged by Hirokazu Tanaka and rearranged for Super Metroid for the SNES by Kenji Yamamoto (who also composed and arranged the music for the Metroid Prime trilogy). Tanaka actually said that when he wrote the music for the original game, he wasn't looking for catchy hooks or memorable melodies, but a specific mood. He wanted to create music that supported the game's dark atmosphere and ambiance. I'd go as far as to say that one of the things that makes Metroid one of the darkest games on the NES was the groundbreaking soundtrack that's at times borderline atonal. If you want to check out the original Metroid game, I'd recommend Metroid Zero Mission for the Game Boy Advance. It's a remake with a ton of added areas, some added cut scenes, and a very different ending. It also has Super Metroid's more varied power-ups and far superior control scheme (only lacking a dedicated downward diagonal aiming button, but you can do it by pressing the upward diagonal aiming button + down) which is a world apart from the very limited controls of the original game in which you couldn't even squat/crouch. The original also didn't have a map system of any kind, and the areas can be very visually repetitive and hence confusing thanks to the old hardware's limitations, so getting lost over and over again is pretty much guaranteed unless you've played through the game a dozen times). I grew up with the original, so it has nostalgic value to me, and I think it has the best atmosphere (likely because of my nostalgia goggles), but if you've never played it, I'd say go for Zero Mission. Seiken Densetsu 3/Secret of Mana 2 is available in English only as a fan translation, but it's pretty good from what I can tell. The story varies depending on who you choose into your party of 3, but the stories I've seen so far I've liked. If you want an example of a game with an absolutely horrible story told horribly to see what NOT to do (and to see how to do a total character assassination of a once strong, badass MC), take a look at the infamous Metroid Other M (although it's a 3D title). I don't think I've ever seen writing quite as heavy-handed as in Other M (come on, just the title spells M.O.M. and tossing the M to the beginning of Other spells Mother, zomg!!1!1¿₩). Just don't ever try to make a drinking game out of downing a shot every time you hear the word "baby" during the first few cut scenes. You wouldn't survive it.