Andrew,
Ensuring as consistent experience as possible across the different clients (ArcGIS Explorer Desktop / ArcGIS Explorer Online / Web APIs / iOS / ...) is a high priority for ESRI. We're in a good position to do this because none of the above applications/APIs are on the same release cycle as the main ArcGIS Server platform which means we can rollout new functionality on a more frequent basis.
Regarding getting other data into ArcGIS Explorer Online - the current options are ArcGIS Server services and client-side generated content in the form of Notes. These Notes once saved into the web map will be available in ArcGIS Explorer Desktop. Unfortunately due to some limitations with the underlying SilverLight technology we were unable to provide any local data support (e.g. File Geodatabase) in ArcGIS Explorer Online in the current release. This may change over the next few month/years as both SilverLight and ESRI software make advances. ArcGIS Explorer 1500 will bring some new capabilities for sharing content with ArcGIS Desktop users and other ArcGIS Online users.
The ArcGIS for iOS is a new release for ESRI and so I would expect to see that platform evolve, and likely very rapidly, in the short-medium term as we begin to really exploit the full capabilities of the platform and understand more about what our users would like to achieve in this client environment.
ESRI are also working hard at making ArcGIS Server more affordable, both in terms of making addtional functionality available in lower license levels of the product but also exploring new deployment routes such as the recently announced Amazon EC2 cloud-based option, and lastly other programmes such as Enterprise License Agreements and the ESRI Developer Network (EDN).
I'd encourage you to approach your account manager with your requirements and budget and see what they can do to help.
Regards
Mike
