FMTouch is a very nice app. The main thing it has over FileMaker Go is syncing. They created a fantastic way to sync between databases.
Otherwise, FM Go takes it. MUCH broader support for calculations and scripts, and at least in my experience, it's much better and handling larger databases. It's also much more simple to use. Getting a database from your computer to your phone with FMTouch is a bit of a pain. With FM Go it's as simple as copying the db over.
If you have more specific questions, feel free to ask, but I'd go with FM Go.
I think the filemaker engineers figured most users would link to a database hosted by filemaker or filemaker server via 3G or Wifi instead of synchronizing files...
Yeah, I'm just not sure why they'd assume that. Or maybe I'm not most users. The last thing I want to do is rely on my iPhone's connection, as well as the internet connection at my office (which goes down almost every weekend). Syncing is much easier and more efficient for me.
But, such as it is. I still like FM Go.