Expanding the points made in Compression and Compression in Languages up to the Methodology level, and beyond.
Above languages we have design methodologies and team management methodologies, and the trade offs continue. A methodology that works great with a team of four may crash and burn with a team of 400. A methodology that works well with that team of 400 may have horrible overhead for the team of four.
One common methodology trade off, not just in software, is to improve consistency at the cost of creativity and spontaneity. McDonalds uses this to their advantage, because they are all about consistency and not at all about creativity. Managing your programmers like a McDonalds is a recipe for disaster under most circumstances. Managing a McDonalds with an Agile methodology is little more than an amusing mental image:
Hello, welcome to McDonalds. We are currently not serving hot food while our chefs refactor the grill and deep-fat fryer to use the same heat source, and our drinks won't be available until Bob completes running the unit tests to verify that we haven't accidentally caused our fountain drink system to dispense boiling hot oil... again.
When I pointed out that software is unusually hard to find a single good methodology for, here is where the problem manifests; it isn't that you can't produce a good methodology, it's that there doesn't seem to be one methodology that works across the entire domain of project scale, resources available, and other business pressures. Usually when someone is rhapsodizing about what's wrong with software and how to fix it, they will propose extremely heavyweight methodologies involving vastly more design and testing than is typically used in a real software project, which is all find and dandy, but such things are very, very costly. Can a methodology that virtually guarantees that you will run out of money and go out of business before completing your perfect gem of a program actually be considered "the answer"? (Hint: No. Once "practicality" is discarded as a judgment criterion, who really cares about the rest of judgment?)
Every methodology's performance varies along many axes depending on the circumstances it is applied in, and the people who apply it. Bug rates, code output, code quality, cost, none of these are independent variables. If you want effectively bug-free code, you'll need a very expensive methodology. If you want a cheap methodology, prepare for either low quality or quantity of output. And so it goes for any number of different combinations of criteria.
Nothing is free. If a methodology makes it easier to obtain one type of result, it makes it harder to obtain another type of result with the same resources.