Group layers as in, for example, I have several layers that make up our complete storm sewer system. I have each of those layers in a group, turned on, but the group itself (the group has a layer number in REST) is turned off. It's just an easy way to turn on or off multiple related layers. So it sounds the same as the issue you described with scale-dependency.
I can see the use of popups. Ideally I would like to use a mixture of popups and identify. I just don't see popups being the only way to go. I have many layers, and some of them just have way too many fields to show in a popup....or things would just be cleaner to have a popup with key info and identify for more in-depth details. I can just see it being such a mess to have something pop up no matter where you happen to be pausing your mouse.
I still find it strange that an identify tool (one that simply functions just like they do in ArcMap - how is that too much to ask from esri?) isn't built into the viewer. To me it's the single most important thing in mapping outside of the ability to zoom.
I'm scared to even ask this but should I be using a different viewer other than Flex? Is one of the others more identify friendly?