Interesting question. Skipper Canteen can be a lot of fun, depending on the server you get. Some of them tell excellent jokes and interact really well with the guests, others not so much (or perhaps they have more tables to serve at the particular time). Skipper Canteen is fun, as you say. The menu is funny all by itself. When we have been there the last few times, seating was very slow; but that was at dinner, not lunch. The menus appear to be identical for dinner and lunch at both places. The Kungaloosh dessert at Skipper Canteen is excellent. I've had the "Tastes Like Chicken" multiple times. I have found it variable in crispiness and spiciness.
I don't know whether the Beast greets guests at lunch--maybe? I think all of the dining areas at Be Our Guest are lovely. Personally, I prefer the Ballroom, even though it is very large and open. The scenery and decor are gorgeous. I think the food at Be Our Guest is one level up from Skipper Canteen, but so are the prices, depending on what you order at Skipper Canteen. Be Our Guest has a prix fixe menu, with options. Where did the grey stuff go? I don't see it on the menu.
Be Our Guest has an interesting entry. In our experience, you are not admitted to the front of the "castle" until they are close to being ready to seat you. Its entryway is more elaborate than Skipper Canteen's, though Skipper Canteen also has interesting items in the waiting area.
Personally, I'd go with Be Our Guest, expecialy since you have been interested in going there for quite a while.