At the risk of appearing partisan, I'm completely the other way around on this!
I find London's butterfly house a nightmare - one of my absolute least favourites - too cramped, too claustrophobic and too busy. I eventually managed to get to the puparium on my last visit but it took some effort (the previous two visits I don't think I even bothered to go in, which is unlike me!). Chester's allows much better flow through the building with its multiple paths, and although the species line-up varies they have some real crackers in there from time to time (I really miss http://www.zoochat.com/42/golden-birdwing-chester-19-02-12-a-259672/ and http://www.zoochat.com/42/common-green-birdwing-258607/ !). I also prefer the more solid structure rather than the polytunnel. There are normally volunteers in Chester's as well - possibly not midweek?
In fairness to ZSL, Whipsnade's butterfly exhibit I like much more, for similar reasons - light and space to move!
I actually think London does pretty well these days in adapting to its site (though I haven't seen the lions yet). Chester has always had the luxury of land since its early days, and of course still has more land it can expand onto if it wants to.
Glad you saw the Tuatara - they can be a bit hit-and-miss.
I think the thing with the boats is that most people go on them, but once - so a busy day they're packed, a quiet day they're, as you say, a bit forlorn - the old Waterbus of course just wouldn't set off if there were no passengers!
I personally think the Twilight Zone/Fruit Bat Forest, while it has had a few tweaks and amendments over the years, is the most successful exhibit Chester have ever built - from memory it's 18 years old now (anyone feeling old?) and still one of the best things there.
