First of all, trying to design a system without knowing the requirements will drive you insane if you are expecting any semblance of quality in your architecture. I know this because I've tried. My previous attempt at creating a game engine went down in flaming glory because the end result wasn't as flexible and usable as I had hoped. Before you write a single line of code, I implore you, write a design document for your project. Describe what the system needs to do in detail. Why is this so important? Without this step, you're essentially flying blind. You will re-factor your code three times as often, bloat your code base including features you don't need; and if you're like me, you'll agonize over finding the Right Way to do it--except you won't, because you don't know what you need.
Case in point: in my first engine, I rewrote my resource manager four times. Not a simple re-factor mind you; a complete rewrite. I included features like loading from a separate thread, which is a great feature, except that I didn't really need it. I just thought it was cool and that every engine should use it. Granted, I learned a lot about what I did need during those four rewrites, but I would have been better off starting with the essentials and refactoring from there. I went into it without fleshing out how the end product would use the system; as a result, my design suffered from code bloat.
Build a (Good) Foundation
I've heard differing opinions on this, so take it with a grain of salt. I see a two specific mistakes that neophyte developers make (including myself) when they are just starting a big project. Either they try to sketch out the entire system (a large one, mind you) on paper, in detail, including every major class and how they'll interact with other classes; or they don't attempt to design anything and just start coding. The latter is just pure laziness in my opinion--the chances of designing a good system with that strategy are akin to winning the lottery (unless you're John Carmack). The former, however, is just as destructive. From my experience, trying to build exclusive from the top down is paralyzing. You scrap design after design trying to find the perfect one (hint: it doesn't exist).
As with all things in life, good design comes with moderation. Begin with your requirements and write some hypothetical sample code of how you will use the system. One good way I've found is to write a bogus program (or part of one) in pseudo code, testing out various interfaces and ideas. At the same time, begin building the foundation for your system. If it's a game, start with the basics, like a basic map loader. Just get something working.
Break Down Work into Manageable Chunks
As you build the components of your system, not only will the next step become more clear, but so will the requirements. You'll realize something you need but couldn't have known early on in the process. This allows you to refine your requirements as well as your code. By starting simple, you will save time refactoring and gain momentum and efficiency. I see many developers who attempt to write hundreds of lines of code without ever compiling it. They proceed to spend hours trying to get it to even compile, and then twice as many working out the bugs. This is not good practice; a better method is to utilize unit testing. This is the process of writing small chunks of code and then rigorously testing it before moving on to another component. This gives you confidence in the components of your system as you build on them, and boosts your morale as you see small parts working independently. Furthermore, it simplifies bug fixing since you can focus on one part of the system exclusively.
Pick an Achievable Goal and Stick to It
This is probably the most important point. Avoid the pain and suffering of trying to design the perfect system for any product. It won't happen. Always know your requirements and design for that only. This is especially true if you are trying something new. I don't personally know how the guys at Epic designed Unreal 3 or their story, but I would imagine they built it up using the good parts of their games. Not only that, but the guys developing Unreal Engine 4 are probably the same ones who built the previous three engines (at least the lead developers). In short, defer your amazing do-it-all project for when you actually know what you're doing (I say this to myself as well). Most of us started out wanting to develop the best MMO on the planet; we quickly realized this was foolish. However, some of us are repeating that foolishness on a smaller scale. We're trying to build something we have little experience with, and make it better than everything else out there. That's just my opinion.
How does this apply to me? Well, a lot. I'm trying to trim down my grandiose plans to something manageable. For instance, what are my goals? I've spoken about those in recent blog entries. If you go back to my first blog, you'll find that I've trimmed it down a bit since then. I may trim it down even more. As a humble hobbyist with only 10 or so hours a week to devote to doing what I love, this has to be the way it is. It's just reality.
Anyway, I hope this was helpful. Again, it's just my opinion, and I'd love to hear your feedback if you agree or disagree. Thanks!