There are two major differences between MSI in SFDC and MSI in Outlook. 1) In Outlook there are no folders to organize the emails and 2) In Outlook the email tokens don't resolve.
Also for my company 3) In Outlook, the email server appends an email signature to the bottom of every email.
Therefore, the Outlook plug-in would be more useful if we could create versions of the email templates specifically for Outlook and leave other emails unavailable in Outlook. This would help 1) Keep the Outlook email templates to a minimum for better organization and 2) ensure sales reps don't send the wrong artwork or artwork with tokens through Outlook.