This is kind of part of the make your own guide to creating role playing systems. This also stands alone, however, and is interesting on its own.
A sure way to make games more fun is to have an underlying principle that drives the game. This will make the game's fiction more coherent, and the rules can often be part of that fiction.
As an easy example, here's a wacky "science" video. A game could be easily made with this as its underlying principle. This would allow for a "convincing" simulation of species, landmasses, etc. Also, as you start to think about what makes the planet grow, you'll have to come up with an interesting set of physical/metaphysical reasons that will drive the biology, technology, magic... whatever parts of the setting you want. The game would feel very cohesive, and a big part of it is incorporated into the rules - the rules for tech work the way they do not because of some arbitrary reasoning, but because it all fits into the underlying principle.
When you're designing any game of any type, above and beyond the rules you use is how coherent yet diverse the "pattern" of the game is. The easiest way to make a pattern coherent is to relate every bit of it to a specific theme. You don't even have to state the theme - actually, it's generally better not to state it, at first. The coherence will still be there, and players will still feel that the game is "well designed". Long experience has taught me that they can still tell that all the content is "pointing" towards something.
Obviously, the principles don't have to be something so dry as a scientific theory. You might explore an emotion, or the meaning of honor, or the fact that transforming robots are way cool, but the basic idea is that everything in that game is related to the principle. Every character, every piece of setting, every game rule... designed to explore the ramifications of the underlying principle.
I can't stress this enough. Even lighthearted games benefit from underlying principles. Even card games, Flash games, drinking games. The theme can be serious, it can be stupid, it can be funny, it can be scary. It's simply a magnet that draws all the pieces of the game together.
Do you know what I mean?