When you use more than one transformer on the same layout, the traditional recommendation was to phase them, by adjusting to the same voltage and connecting appropriate outputs together to see if you got a strong, spark, or no spark at all
With the adoption of plugs with a larger and smaller prong, is that problem eliminated if you simply change all the plugs on your transformer?
No, it complicates the issue.
In what way is it more complicated?
I need to replace a plug, and what I see in Home Depot all has a grounding 3rd prong, and the two flat prongs are of different widths.
Well, run through your procedure of replacing the cords.
-Will you use some kind of convention as to where to connect the ribbed vs smooth conductors?
-How will you assure all transformers can be phased to yours with the new plugs?
You should search the Home Depot or Lowes web sites for “non-polarized plug” to find the ones that are non-polarized. They are still available (though certainly may have been out of stock at your store when you looked). No third prong, no wider blade.
(when I just checked, the Lowes search engine seemed to do a slightly better job of filtering them to show the actual non-polarized ones).
Don’t make the phasing process harder than it needs to be. 
As Rob said, it’s much simpler if you stick with the non-polarized plugs on the old PW transformers.
Especially if you ever decide to mix them with a modern transformer, as the modern transformers will of course be polarized plugs, and it would be much more simple to phase the old PW to match the modern one than the other way around.
After phasing my 3 ZW transformers I replugged them with polarized plugs to insure they would always work correctly. A 3-prong plug would also have worked.