Disclaimer: I sell SeaDek for a living.
Like some other things in life, It is not for everyone, and it is not for every boat. Some folks hate it, some folks wouldn't run a boat without it.
I'd recommend starting small and just doing your poling/casting platforms. 2k for a 16' skiff is high - that must be for a full kit (every inch of the boats walking surface). Start with those small areas, see if you like it, and add on down the road as needed/wanted.
The biggest thing to watch is how the install is done. Prep work is everything. If your installer cuts corners, you will have issues down the road. If they do the proper prep/cleaning and install techniques, the SeaDek will last 9+ years. Also, ask questions about warranty issues. A quality installer will come out to do any removal/replacements necessary for you should any issues arise.