When presented with the "Warning" window for when the 'Host Key does not match', it would be useful to see the key(s) that have been saved for this host (ie: what was expected). A simple way would be to have an extra button "Expected Key(s)" that displays a new dialog with the host key(s) expected for this connection (and a way to copy them to the clipboard), rather than the one provided by the server that you're connecting to.
In this way, you can provide the host admin details of the old and new keys in the case of an change rather than just the new key. This can really help when it's due to an unexpected change (eg: finding and restoring an old key and confirming it's been restored correctly).
It would also be useful to have some sort of admin option so you can manage any saved keys (eg: so you can go through and remove old keys) without having to either edit the registry or config file manually, but this is lower priority.