We changed this in 9.5 because it was something a lot of our users had requested over the years.
As you have found out, you can get the previous behavior if you enable the Show Only Default filter. We have an open ticket for making this setting available also in the Options area of the Connection tab (and in the Create Connection wizard), which would make it easier to enable or disable for a number of connections using Database->Edit Database Connection(s). I have added your vote for this, but for now this is something that you unfortunately have to do for one connection at a time.
I recently upgraded to 9.5 and recognized a change in the navigation tree: I open a database connection, expand "Databases" and now see all databases that the user I'm connected with is able to see. Those are a lot in my configuration. In former versions of DbVisualizer the results where already filtered to onle the one database matching the name of the connection or whatever, at least only one database was shown.
I can get the old behavior if I right click on "Databases", select "Database objects filters" and "Show only default...". But it seems that I need to do this for each of my connections, which is very annoying.
Is there any way to get the old behavior back, so that ALL of my connections use "Show only default..." by default?