You could do FME Server and set up an automation with a directory watch as a trigger. So any new file placed in a folder will trigger the workspace to run. You're probably going to have to add some logic to the workspace to deal with unexpected input though. I.e. if a user uploads data in the wrong format or the wrong schema you want it to fail nicely rather than crash and/or corrupt your database.

Scheduling can be handled with FME Server as well.

The benefit of FME Server is that you can serve a larger group of users and through automations you can build some pretty complex workflows.

The amount of automation and possibilities that come with FME Server are amazing. If you have the budget I would definitely recommend it for automating these tasks (and many more). Schedules, emails with attachments, Directory watching are all popular methods for triggering a process.

Great thanks for the feedback. Would you suggest putting the files initially in a folder structure for FME server to pick up or are there any other alternative methods that could be used?

I do like the folder structure aspect and FME server can just simply pick it up. Other options I seen are things like web pages where people can upload and then have a FTP server where files go for FME to maybe pick up. Sharepoint is another option.

Where do you usually store the files before FME picks it up? A shared folder area or any other options?

FME Server is flexible, however, a shared folder would makes sense. A baked up filesystem would be my recommendation. FME Server comes with it's own folder structure for logs etc as well as places for data which you can use. But in addition you can set up shared folders and even connect to s3 buckets. If it were me I'd probably set up one shared connection per project to keep the data separated on your network share. If working in the cloud then go with an s3 bucket.