The instruments name became outputs which helped define what they were.....as most of the time you're thinking I've got this 'thing' where am I going to hear?.....through an output of course.
The mixer window used to be called the instrument window.
That is why it uses the command I to bring it up and this was retained as command M was for markers.
As far as effects or VSTi's are concerned you have 2 options.
Sticking it onto an aux or sticking it directly onto the track you want it on.
All beginners would probably go for the 'on the track' option.
Originally you would select your track
Hit command 9 and command zero to bring up the plugins and effects windows, and drag the plugin needed to the effects/synth window.
Now as Jerm says you can choose something directly out of the graphic editor window.....but this operation is still moving the plugin to the effects window (it's doing it for you).
The aux is there to allow you to run an effect like a reverb on more than one track thus saving CPU......as you don't need to run multiple instances of it.
Changes like the instuments to outputs or instuments to mixer names and accessing synths from the graphic editor are mostly forum requests that Jerm has taken on board and worked his guts out to implement.
(The one he sweated the most over was multiple undo!
)
If you can think of other things Metro needs suggest them and he'll probably put them in within 30 days............he's a bit of a genie. lol