So far, the flooring is holding up well (three seasons). With Flexiteek, you really need to have someone knowledgeable doing the install otherwise you can run into problems with "bubbling" or air pockets (so I have been told). We used some folks on the St. Croix (JL Boatworks) and they did a fantastic job :
https://www.jlboatworks.com/maintain-protect/flexiteekOne thing I hated on my Glastron prior to the restoration was the non-skid material they used on the top of the deck lid. Great at keeping you from slipping but also impossible to keep clean and great at trapping dirt. Also, I use this boat a least a couple of times a week to go fishing and I was sick of pulling hooks out of carpet. Couldn't find a way to Flexiteek the casting platform in the bow, however.
One item to consider, however, is weight. Flexiteek is pretty lightweight but still adds weight. I believe this Glastron had a dry weight of about 2300 pounds and with the changes I've made (primarily swim platform but also the flooring and fiberglass) I would guess that I am running closer to 2800 pounds dry weight and then probably closer to 3000 pounds with fuel and gear.
I had to upgrade my boat lift capacity after these changes, so beware!