This is what I plan on doing. I've enjoyed writing and drawing growing up having written a few short stories and half of a novel recently. I am currently teaching my self to draw pixel art and plan on creating everything from this game from the ground up. Story telling is something I really enjoy. I know that it is a huge task to take on, but again for me that's the fun in it.
Again, I'm not trying to jump into it full force and complex without any experience, I do want to work on some smaller projects, work through a few gaming books and get comfortable and then work my way up to a more complex game. As I've mentioned, I've learned a lot in the past few days already, been working on sample code to accomplish certain ideas and researching a lot. Thanks everyone for your advice!
If this really will be a longterm project for you, you might want, after you learned the basics, and feel comfortable with unity (given you invest the time to learn its features, it really is a powerful tool), invest some additional time thinking over you options before embarking on "your quest".
There are certain pros and cons to different ways to approach your task, and you should really think through what you can compromise on, what will support your vision better before you commit to something. Maybe even start a small mini project to test your ideas (Vertical slice) to see if your decision is a good one.
Examples for topics to really think through:
1) 2D vs. 3D: I know, the general word is 2D is easier than 3D.... though this is only one part of the story. Truth is, 3D always has some overhead, because there are more minimal steps involved to get something working. Thus for SIMPLE graphics, 2D will be clearly far easier to get your graphics for.
This all falls down somewhat when you start using isometric views, and want good looking animations for your characters. AAA Quality 2D Graphics is just as expensive and time consuming as AAA Quality 3D Graphics, if not more.
You should really think about what you want to achieve here. If you want to stay as true to retro graphics as possible (for example SNES Era)... go with 2D, maybe even with pixelgraphics.
If you just do that because you think it will save you time and money, or you are trying to go for the best 2D Graphics you can achieve, really think hard about why you wouldn't want to give 3D graphics a try.
Lets be honest: AAA graphics are out of the reach of any Indie. Creating beatiful HD 3D models is a huge timehog, and needs and aweful amount of skill, or money if you buy stock art.
Simpler 3D graphics are not THAT hard to achieve though. And there are a lot of people that are decent at 3D Modelling, but can't draw at all. It might be that your target art style can be achieved easier in 3D than trying to do it the 2D way.
The good news is: if you learned to use Unity, you have both options. You can try out what will fit your project better.
2) manually build vs. procedural content: this can REALLY cut your work in half (or even more), while giving you the ability for additional gameply options (procedural dungeons come to mind).
True, you will have less control over the final outcome, but there are many ways to utilize procedural content. The extreme, having dungeons and levels be procedurally generated during the game, is only one option. You will already gain a lot of productivity by letting a procedural generator generate your level in the Unity editor, giving you still the possibility to give your generated level a manual finish after.
For some things, procedural generation can even achieve results that are near impossible by hand. I for example run all of my roughed out level terrains through a World Machine network that will create beatiful heightmaps with realistic erosion out of a rather naff and rough input heightmap.
Good news here is: there are a lot of free or not-too-expensive tools for procedural content generation for various tasks on the market, as well as Unity plugins for ingame procedural creation. You do not have to write everything on your own.
These are just examples. There are other things you will have to think through... but of course, you will have some basics to learn before these questions really matter.
Just be aware you are talking about a project here that will take you years to complete. It might be a fun journey, but it will be a long one. All left to say is: Good luck on your journey, and enjoy the ride! :)