Spoiler: I didn't end up using Mark's idea in Do, as awesome as it was. Here are some reasons why, completely unrelated to the quality of the idea itself.
Explain your rules better before changing them.
It takes some experience before you can recognize the difference between a poorly designed rule and a poorly explained rule. Assuming you do know the difference, be aware of the temptation to add new rules to fix a perceived bug. It could be fixed just as easily by offering strategy or style advice as a non-instructional sidebar. That is what I ended up doing in Do. Instead of adding the new rules for stone usage and naming, I just asked my players for their advice and tips on picking good names.
Stick to your goal.
This is probably one I'm most guilty of breaking and why Do has taken such a long time to finish. I started with a loose desire to emulate some aspects of Avatar: The Last Airbender. Gradually that morphed into a number of different goals for the game, but none fully concrete. In the end, it was developing Happy Birthday, Robot! that gave me an achievable goal for Do's development. Do: Pilgrims of the Flying Temple is a storytelling game. It's not a role-playing game. And that is okay. Now that I know what being "done" looked like, I just have to get there.
Better is the enemy of done.
As many smart folks said already. When you work on a project a long time, it is tempting to look at a new idea as the solution that will finally bring it to an end. However, a better unfinished game is never as good as a flawed finished game.
What you're working on is not the last thing you'll work on.
If you don't use every idea you have right now, those ideas are not lost to the ether. In this case, Mark's idea lives on in an email conversation, a blog post, or a future supplement for Do. It is important to write down and save your ideas, but also share them with others. If you really feel this idea is a good, share it. Let other people comment and contribute. You can always pick it up again later for a future game, but even if you don't, at least you shared something you're excited about.
A great idea can start a project, but only work can finish it.
Or, in other words, "Shiny starts, but rarely finishes." To put it more cruelly, a shiny new idea can send you right back to the drawing board. The longer you work on a project, the more tempting it is to add ideas you come across later on. Each new idea is a detour along that project's development. It leads you in a new direction, maybe, but it probably doesn't get you closer to an endpoint.
The solution that gives you more work might not be a solution.
Some designers like to say that if you're trying to solve a design problem by adding stuff, you're not really solving the problem. It's only be streamlining and minimizing that you will find a solution. I don't know if I would be that hardline about it, but certainly it's a red flag if your latest new shiny idea is one that prolongs the timeline by an extra month, then six, then twelve, and so on.
But now I'm beginning to repeat myself, so here are some smart people talking about this stuff.
» Ryan Macklin: The Siren Song of Cool
» Ryan Macklin and Paul Tevis: Cool Revisited
» Brilliant Gameologists: Gamers Are Lazy SOBs (BS)
» Jared Sorensen: Better is the enemy of done.