Disclaimer that this is from the perspective of someone who helps people who call in to NI with problems rather than a developer
If you have not built an application using RT/FPGA, are very familiar with DAQ, and do not need to use the FPGA for any of the reasons smithd mentioned I would agree with using the cDAQ controller. You'll probably save a lot of development time if you stick to something you're comfortable with.
In terms of general use and debugging for your real-time application, it will feel very similar to testing and debugging a windows application. When you click the run arrow on your VI it will deploy code to your target (minimal time) and you will be running your code interactively which means the application is running on the remote target but still gives you access to most of the normal debugging tools. When you are done and want to deploy an executable, you can build an rtexe and set that to run when your target powers on all from your project. You can troubleshoot this the same as you would a debuggable executable running on a separate computer.
FPGA is a separate beast and it does add to development time as people have mentioned, especially if it's your first time. I think RT is pretty good once you get past the whole finding the target in MAX part.
-Matt J