I don't have a CV16, but do I have a 2001 Glastron 185 Ski and Fish and it is awesome for fishing (freshwater - typically walleye, pike, smallies, crappie, etc). I spent a lot of time going to boat shows prior to restoring it to see if I could find something I liked better and I could not (for my needs, anyway).
I haven't done a lot of saltwater fishing (primarily salmon fishing the Dixon entrance in British Columbia - Boston Whalers with downriggers) so not entirely sure what your needs might be. My boat came stock with -
1) Livewell
2) Trolling Motor mount (12v)
3) Cheap crappy rod holders in the gunwales.
4) Bow that is convertible into a casting platform
5) Fish finder
Customization / Upgrades I made :
a) Upgraded trolling motor to 24v
b) Ripped out rod holders and plan to replace with RAM Mount removable configuration during the off season (I'll post pictures when done).
c) Installed rod holders under the deck lid (can fit up to 12 7' fishing rods). Added lock to deck lid.
d) Customized dash to have in dash electronics.
e) Added another set of fishing electronics in the bow
So, I can do pretty much anything for fishing in the midwest and the nice thing is that I can take things off the boat to maximize room for tubing or whatever. The only thing I can't do easily is troll with my I/O at 2.5 mph. The slowest I can troll is around 3mph with the big motor and the trolling motor (24v MinnKota Terrova) will go about 2mph. If I need to troll at 2.5 mph, I could deploy a drift sock and troll with the I/O. But, I don't troll a lot anyway.
Not being sure of what your needs are, as a first suggestion I would spend some time out at the RAM Mount site and take a look at all the cool options they have for mounting things but then being able to remove them when you want to be in ski mode. If I was salmon fishing out of a CV16, I would want a big Yeti cooler for the fish, some flush mount rod holders that could be removed, a drift sock, and some good electronics I could mount on the dash and still remove and hide wires/connections, etc (or leave the electronics in). I would be trolling for these fish.
Hope this helps! Please post some pictures when you're done! Always inspired by what people on this site do to their boats!