There were several other differences as well.

Already mentioned:

..Walschaert Valve Gear - As far as I know used on every Willie. Lima only used it on a handful of Shays, usually using Stephenson.
..Turned valve chests
..Cylinders mounted farther forward - I don't think this had to do with the valve motion, I think the Willie builders just decided it was a good idea.
..Inclined truck springs - Gave a better ride.


Other differences:

..Piston valves instead of slide valves on superheated engines - Shays used slide valves until the introduction of the Pacific Coast models, which copied many of the Willamette changes. Only 2 superheated Willies were built with slides and they were quickly retrofitted with pistons, if I recall right.
..Improved crosshead guide and crankshaft support
..Welded boilers - I have been told that Willamette made very tight boilers that were all or mostly welded.