Personally I like CC to open in my current VS shell when I am using it to diff files in my solution (or against previous version in the solution).
Specifically I like it to open in the VS session where I triggered it from, ie by right clicking in the solution explorer.

Conversely in all situations where I diff files in explorer or any other file browser I want it to open in a standalone window. Both for file diffs and folder diffs.

Obviously I accept that my desires won't match all (or possibly even most) users' but a few config options would help meet all needs.
Usecases I would expect are:
- the one detailed above for VS host of VS triggered diffs and standalone for all other trigger sources.
- VS only
- Standalone only
- most recent shell
- standalone for folder, VS for other
- VS for specific files (eg *.cs, *.cpp, etc.)

Example options off the top of my head:
1. Always open in standalone Shell.
2. Always open in triggering shell (eg VS)
3. Open in shell based on extension filter
4. Default to most recently accessed viable shell (ie in the latest VS or CC shell)
5. Default to standalone shell
6. Always use default

if 1 is selected then it's always the standalone, if 2 is selected and the triggering shell is not a viable one then 4 or 5 will determine what shell to default to. 6 will decide whether the prompt dialog showes or not...