Why so few osilloscope with dedicated isolated channels?
Why are there so few bench osilloscopes with dedicated isolated channels?
  Is it a design issue, a cost issue, a business issue or is it just better with differential probes?


It is a cost (price) and demand issue. Most users don't need isolated inputs.
Most users have ground-referenced signals so a scope with non-isolated inputs is OK.

Cost is an issue as isolated inputs require more complex circuits compared to the standard solution. This makes the oscilloscope more expensive.

Also note that isolated inputs and differential probes are different things! You can use an isolated input as if it is a differential (floating) input but it's not really the same as the connection on the oscilloscope is a BNC connector which is a single ended input. The two electrical connections on a BNC plug aren't precisely the same, one is also the shield, the other (inner connection) is shielded. For DC and low frequency that usually doesn't matter much but for higher frequencies ore low noise measurements it can matter. Then a true differential probe is the better option.