It doesn't make sense to use something that isn't tied to your MIS, so unless it's really unusable the user should try to learn it better and live with it.
It will end up being more work in terms of support and config if you use something separate and then try to recreate functionality and / or take data from your MIS, it will end up being a hassle and you'll probably move back. Unless you really are happy with just a basic spreadsheet format or something.
The benefits of the built-in system are the reporting you can get. I know here they like the brownie points i'm sure it's the same elsewhere.