Yes, there are still some serious issues with the outliner, despite all the work being put into collections. I have been banging on about these issues for years, but for some reason, Blender users have just gotten used to the renaming and layer workarounds, so it has never gotten much attention. Anyone that comes from another 3d package that relies heavily on it’s scene tree like C4D or XSI will find Blender’s outliner very frustrating! And I am am no Blender newb, having been toying with it on and off for 15 years or so, and it being my main gamedev modelling tool for the last few years.
The addition of collections in 2.8 has improved the ability to organise your objects by being able to nest collections within collections. The odd thing is that while collections can be re-ordered at will (and don’t have to be ordered alphabetically), the objects within the collections still have to be ordered alphabetically. Also, while there is still the option to disable the alphabetical ordering in the outliner, it just forces the objects to be ordered in the order they were created.
The way this should work, is that objects would be listed in creation order by default, and can at any time be re-ordered via drag/drop (as collections currently can be). The “order alphabetically” option would then be a command that can be clicked to reorder the items in the current selected collection, rather than being an always on toggle mode.
I also don’t think that having a flat hierarchy in the default collection mode was a good change, and was better with the earlier versions that showed a full hierarchy. When you switch modes to see your hierarchy, you lose the options to filter the outliner. I can’t help but think this is very counterproductive. I realise that some users want to have the same object in several collections and this is the reason for this decision, but there must be a more flexible way of going about this. I personally would only use collections much like I would use nulls in other software, as a way of grouping object hierarchies (one object only belongs to a single collection or sub-collection). Of course other users may prefer the existing workflow. Both types of users should be accommodated.
The other multiselect issues in the outliner have been mentioned many times before so don’t bear repeating. It feels like having a professional level outliner is finally within the grasp of 2.8, so I am hoping that it will see some more polish before it’s final release!