Depends on your use. iPhone app does a pretty good job keepijg you organized. Web app offers many resources. I personally. Base it all on the iPhone even though I have access to my desktop most of the time. Somehow, I find it more convenient. Then, I use the web app mainly to create smartlists and notes.

The iPhone app gives you offline access to your RTM stuff, which can be handy in some situations. You can look up or process your stuff offline if you happen to be somewhere with no WiFi or data access over the cellular network. I ran into this very recently when I was running errands at a Target store where my iPhone didn't even get Edge. You can sync with the cloud the next time you have online access.

With the mobile version, you always need to be online. I never use the mobile version, since the iPhone app is more than sufficient when I'm on the go. I assume you're talking about the mobile web version.