In the real world, software works for you.
In GIS, you work for the software!
It’s not to say you can’t get value out of traditional GIS packages, just that you’re locked into doing things their way. I was just about to write a clever analogy but I think I’ll keep this simple. When in your GIS package, you generally are limited to only their processing tools. While this does allow you to gain familiarity with their use, you end up making compromises to get things done. You can buy your groceries at the gas station convenience store, but you have to work hard to make it all happen (wait, did I just use analogy anyway?). It’s at the supermarket where you can choose from 20 different kinds of marinara sauce to get exactly the right one.
I really think GIS is like a supermarket. When you do your projects outside of these proprietary GIS applications, it gives you the freedom to pick and choose which analytical libraries you want to get each analysis done. I can use GDAL, Arc.py, sci.py, R and even some Erdas to get my work done. Just how I’d make dinner, pulling different ingredients from different companies. Just like some nice ziti, you end up with great output and something that works wonderful with your work flows.
My feelings are GIS software should adapt to how I work, not the other way around. You should too…