Inability to bulk UPDATE items without specialized scripts and the API. If you need to change a field on 25 items, you are clicking ~75-100 times. This quickly becomes untenable.
Inability to 'round trip' to excel (via CSV). Related to #1, you cannot take items offline, edit and return to the system in batch. This is a bit of a barrier for some of our vendors who want to process items in their own workflow outside the system. This can only be done with the API and a script.
When bulk ADDING items, inability to assign to a group, only an email address. This can only be done with the API where one can add based on a GUID for the group.
In general, the web gui method of adding items from csv becomes unstable over some number around maybe 100 (?). Additinally, the errors that pop up only last for a few seconds on the screen so you completely miss them if you aren't intently watching for several minutes. The workaround is to open the developer console for the browser - but this is not something normal people do.
Usage statistics, any custom dashboarding or any view across projects must be done in powerbi with the API.
Useful functionality