There are other things that can differentiate the process in different distilleries, such as:
The material that various implements/machinery is made from: i.e. wood or stainless steel etc
How wet/dry the barley is after malting
Whether the germinating barley is turned by hand or mechanically
Whether water is purified or filtered before use
Size of the batches made
Whether water is reused in mash-tuns
Whether organic ingredients are used
The extent to which the process is automated or decisions are made by 'real people'
Whether bottles are filled by hand, or mechanically
However the extent to which the above will actually effect flavour is probably minimal.
Then you get into decisions taken by the master distiller that will affect taste:
How long whisky is left in casks
Whether to mix whisky from different types of casks together
Whether to mix whisky of different ages together (multi-vintage)
Whether to mix whisky of different peating levels together
Whether to 'finish or ACE' a whisky in another cask (could be sherry/port/wine, or a different type of wood, or smaller cask)
Whether to bottle whisky from a 'single cask'
What strength to bottle the whisky at (i.e. how much water to dilute it with, if any)
I'm sure there's much more.
For a quick intro on how whisky is made, see here, but there are books that will go into much more detail:http://www.royalmilewhiskies.com/viewindex.asp?article_id=wb_making
My opinion (based on what I've gleaned from books and tours) is that the things that affect taste most are:
Level of peating in barley
Shape of low wine and spirit stills
The 'cut' of the new spirit taken
The wood used and all the variables related to casking
The final strength of the whisky (although you can change this by adding water yourself)