for Wishes, you board the boat about 9:15 at the marina in the rear of the Contemporary hotel. Kids under 11 must wear life jackets.
We first headed out towards WL. The captain talked a little about the lake and area. It was interesting. As you head back towards MK, you stop and watch the Electric Water Pagent. It's kind of neat to see it up close.
From there, you go to the main lagoon. He took us past Poly and GF before lining up just in front of the MK. There were about 12 or so other boats in the area (there's plenty of room - you feel private).
The show was better than I anticipated. The fireworks are very large and very high, so you still get a good effect even though you are outside the park. The downside is the music. You can hear it, and make out the words, but it is distant. You would think that each boat could have some sort of radio to listen to it.
When Wishes was over, we went directly back to the marina.
The kids (9 and 12 - boys) like this better than the Illuminations tour because it was longer and they felt they saw more (cruising around the lagoons).
Note that the experiences are completely different. The Illuminations cruise starts in the daylight (show is at 9pm) - at least in the summer months. You take a quick trip down the canal then take your position under the bridge to watch the show. Since you are actually in EPCOT, you feel like you're part of the show and can easily experience the music and all visual effects. There are only 5 or 6 total boats for each cruise, so you feel pretty exclusive.
The wishes curise is at night. The lagoons are not lit, so, other than the boat's lights, it is very dark. It gives you a much more feeling of an evening cruise. However, as I stated above, you are rather far away from the action, so you are not as fully emersed in the show.
Bottom line - Illuminations cruise is the best way to see Illuminations - hands down. The Wishes cruise is just another way of seeing Wishes, but not necessarily the best (if you want to be fully emersed).
FYI - We purchased the "meal" on the Illumination cruise. this was expensive and overkill. There was a large deli plater that could easily feed 7-10 adults - we barely touched it. For the Wishes cruise, we stopped by the gift shop at contemporary and pick up some chips and pop to take with us. Much more economical.