this kind of thread are what lively discussion is all about. as we keep stressing, there are 1000 ways to "git-r-dun" in this hobby. i know peeps who are always tweaking their systems to add this or that or upgrade something, and they enjoy that. i try to "get it right" (at least what i consider "right" for the setup) in the design and once i'm happy, i stop tweaking and let the system run.
another thing i've learned is to bite the bullet up front and use the equipment you really want to use so i don't end up buying the same equipment twice, such as a skimmer or lighting.
designing a system from the ground up is really one of my favorite parts of the hobby, and sometimes you nail it, but sometimes you see shortcomings. for instance, i have at least two systems that i won't set up the same way when i move them. tried something that i wasn't entirely thrilled with. they work, but they could work better. it's a constant learning curve.