As a Canadian, a feature I'd really like... request no stops in the USA. eg when flying to South America.
(USA is a great country but doesn't get "in transit")
How many countries do? I take it for granted traveling through Europe, but made the 'mistake' of booking a USA->Peru trip through Mexico City rather than taking a lounger journey through Miami, and had to clear customs and fill out a landing card for Mexico. Then it ended up being the same when transiting through intermediate countries in South America. I have so damn many passport stamps from just one trip, where I'm much more accustomed to shengen and EU travel in general.
Perhaps its small countries that do it best. Eg Hong Kong, Singapore. Well, the website needs a database of "in transit" aware countries (or airports) and option to prefer them.
That being said, I would completely love to specify stopovers as the flight path, also completely avoid airlines (even fi they're codeshared). (I.e. Leftouthansa)
I've had fun with airwander.com for looking at potential stopovers -- never booked through them, though, so can't make it an official recommendation.
Usually when wanderlust strikes me, or I'm going somewhere terrible and want to inject "somewhere better" as a stopover, I find myself there contemplating the "ifs"