There are a couple of promising solutions to this type of problem, depending on the situation.
If the problem is that you decide something can be optimized in a certain way and you extract a method or something and realize that because of that decision, you are forced to code everything else in a convoluted way, the problem is probably that you didn't think far enough in the design process. If there had been a well written and planned spec, you would have known about this problem ahead of time (unless you didn't read the spec, but that's another issue :) )
Depending on the situation, rapid prototyping can also address this problem, since you'll have a better idea of these implementation details when you start working on the real thing.
