I lived through both worlds: wet slip and trailering. I wish I had the money (and space) to afford a wet slip AND have a trailer, but I don't. There are so many lessons that I've learned in the past 5 years! Knowing what I know now...
1. If I could only do wet slip OR trailer/storage, I'd choose trailer/storage - in my case. Down here where we live in Florida, there are SO MANY places to go with the boat. When we had the wet slip, if we wanted to take the boat down to the Keys, it required so much planning and luck on weather. It was a two-day trip to get down there (assuming you had a good weather window), and once there, you are at the mercy of the weather in getting home. It's not like we could have just left the boat there if I had to get back to work on Monday. By having the boat on the trailer, we can go to the Keys any time we want to. If we have bad weather, we don't go out in the boat. But we've taken it down 3 times now in the last 10 months, and while the weather would not have been good enough to sail the boat down, it certainly was good enough once we got there.
2. If you're going to keep your boat in the water, you've got to make sure you wipe the pontoons regularly - especially when in warm saltwater. The marine growth - even with bottom paint - will quickly overwhelm you. Down here in the summer, if you let it go for 2 weeks, you've got a mess to scrape off the bottom. It wasn't bad when it was just the dual ellipticals, but when we put the SPS on, it was EXTREMELY difficult to get underneath and clean those pontoons - especially the center and inboard sides of the pontoons. It just wasn't fun. And you had to do it. Mother Nature was going to let crap grow whether you wanted it to or not.
3. If you're going to keep your boat in the water, make sure you keep up with your anodes - whether they are zinc or aluminum - ESPECIALLY if you're in saltwater. As part of your routine maintenance, you need to check them regularly. What an expensive lesson this has been for me. And speaking of which, if you're in a marina, make sure you don't have stray current loose in the water.
4. If you get a wet slip, get yourself a dock box. It was wonderful having a dock box right there at the boat. Very easy to just move anything you need 15' from the box to the boat.
5. If you have a wet slip, check your mooring lines regularly for chafing. We had a cement dock with outdoor decking planks on the finger peers. Just the slow, gradual movement of the boat (tides, currents, wakes) would slowly eat through the lines. And of course you know they'll let go at the worst time possible. Now you've got your boat banging around the dock (or your slip neighbor's boat). Not good. Something that I did that really worked out great was to purchase a roll of Black 1050 Denier Coated Ballistic Nylon - aka Kevlar. I bought a bolt of this fabric (4' x 30' I think), and made 4' x 8" strips, sewed them together to make a sleeve that I ran my dock lines through. The fabric took all the wear and tear from the cement dock, and kept my lines like new. Check your mooring lines regularly.
So I guess in our case, there was really no comparison: by trailering the boat, I eliminate a LOT of work for me, not to mention this mess that I find myself in now.