Thomas,
I have a lot of experience with software development. I love GTD. Even so, I have only been using Omni-Focus for a short while and am still learning. Given those qualifications/limitations, this is how I handle s/w development issues.

RFE's. I have a well-defined process for RFE's. It leads to a final disposition. Therefore, I handle each RFE as an individual project. There are special attributes I track for RFE's. They include number of requests (used as metric of desirability and prevention of duplicate projects).

Bug Reports. Again, I have a well-defined process for a reported bug. Each reported Bug becomes and individual project. Similar to RFE's, each project for a reported bug includes custom attributes to carry metrics and prevent duplicate projects. I am using perspectives to give me views of bugs by severity (used for summary reporting and budgetary forecasting).

For me, the s/w development process may start much earlier than it does for you. For example, my process starts without an assumption that the requested software is financially justifiable. That means a s/w project includes budget for requirements gathering and feasibility determination. Still, s/w development follows a well-defined, fixed process and is ideally suited for GTD management.

Most of my development work is on large, complex systems. Often, this seems better suited to using a folder containing many parallel projects. However, I am not convinced this should be the generally accepted practice.

I use Omni-Focus to track and manage my personal tasks related to the development. It is only one tool in my box of project leadership and support tools. I do not use Omni-Focus to replace the proprietary resource management tools, standard project planning tools (for example, MS Project or Primavera).

I hope this was of some help to you. Don't be afraid to experiment. Let me know what you decide and why. Your feedback could help me.

regards,

Dr. Dave Dyer