Board Thread:Plants vs. Zombies: Garden Warfare 1 & 2/@comment-5079138-20151018125128/@comment-33882984-20160114202255

Well, i can give you the reason for the Engineer's shoelessness:

There is a taunt (a gesture) related to that named "Shoeless".

If the Engineer had a variant with both shoes on, it would render the taunt's name obsolete.

The fact that most zombies miss shoes are likely just a part of their design and it might be there to give them a more "undead-like" look.

But this is just my personal opinion. I am not trying to say it's canon.