Yeah, the problem with RPG Maker and GameMaker is that they are 2D programs and the industry might tend to frown on them and consider them a hindrance in terms of learning today's technology. Which is unfortunate, because as retro as those little programs look, you can do quite a lot with them.
Ogre was already mentioned, and I'll second that. If you want to get up on the more preferred technology, then Unreal or even better, Torque. Gamebryo is another one though I don't know much about it. In reality, it doesn't matter which one you choose. Just find one you like and keep with it. Aside from interface and capabilities, most of the things you learn will translate across programs. It's just like learning a 3D program.
Speaking of that, let me be quite honest with you. You don't really need to have profound art skill to do what you want to do. But it does help, and it's going to make you even more valuable. You need to at least understand the principles of layout and design, lighting, value and texture, etc. I recommend picking up some basic art books... anything for Beginners should go over the basics that I mentioned. Better yet though, I'm sure there are some level design books out there that will cover the rudimentary art knowledge you might need. Check Amazon, I know they're out there.
I also recommend downloading a trial of ZBrush. While ZBrush isn't really recognized by the majority of the industry as a contender for Maya or 3DSMax, my personal thought is that it's worlds easier to understand, and it's far more intuitive as far as modeling is concerned. So if you're just starting out with making your own 3D assets, I highly recommend ZBrush. Again, once you learn how to use one 3D package, it's less of a hurdle to learn the others.
Another option is modding. I just wrote an article about this on my blog, and you can check it out here
. Basically it highlights how modding could help you stand out from your competitors (other job-seekers) and get a job in the industry. If there's a computer game you're fond of, check out the modding community and see if that's something you might like to take part in. It's not going to be as 'stand-alone' as using a big name game engine to make a level, but if you're trying to flesh out your portfolio, showing levels you've made for existing games really isn't a bad way to go. Of course, I recommend having your own original level in there, for your own game idea, just to show them that you aren't dependent upon one type of engine or platform.
In response to your query about game design, personally I think the best thing you can do is start documenting your ideas and your levels. When you go to create your own original level from an original game idea, write up a concept document for that idea, and a design document for the level. Detail as much as possible, and when you've completed the level, reflect on your progress. Did you meet your milestone goals? What did you have to alter along the way? Fill out your own postmortem for your level, and include that, your concept and design documentation, and any other 'paperwork' with your actual level in your portfolio. Because again, even if you decide you don't want to be a game designer, it shows a really advanced mindset on your part, and it tells any prospective employer that you know your stuff, and you know how to be professional.
Best of luck to you.
Creator of Breakout! The Blog for Game Industry Hopefuls