I would try this approach:
(1) Pull the battery, wait ~1 minute.
(2) Reinsert the battery and power up the phone.
(3) DO not start any app, connect it to the charger.
See if it gets warm under these conditions.
What this procedure does, it makes sure that no background app with high cpu usage runs and loads the system down.
If the phone still gets warm, then perhaps you have a hardware problem
(battery, charge control circuit in the phone, etc.)
If the phone does not get warm then the problem is most likely software related.
just my 2c worth
Peter
PS. Some installed apps may start up with the phone (Task killer, etc ?) this may complicate the debugging.