I can't really compare the GMM PE set with the Eduard set because I haven't seen the GMM set up close. All I can say is the Eduard set is about 5 frets of PE. Some years ago, I did the 1/350 Arizona using Tom's Modelworks PE sets. Eduard came out with a set for the Arizona about two years ago. Eduard's set had a lot more than Tom's did. I've also used Eduard sets for my armor builds. Their sets seem to be very inclusive. Have you seen this site with their review of GMM's Missouri set:
http://www.modelwarships.com/reviews/pe/gm_etch/350-4/missouri.html
Don't let the pictures on the Eduard site fool you. Apparently, the modelers for Eduard just quickly put the PE on the models for display purposes. You're right about the holes in the deck from the ladders. They have to filled in. Here's a picture of my work:
You'll notice the white styrene that was used to fill the void. It's time consuming and slow going but I think it's worth it.
-Jesse