Then again, this is Canada - sensible decision making in military procurement just isn't something that happens here.
But the economies of scale are such that at least the $$ isn't completely out of whack (for purchase at least, maintenance I'm not so sure of). I would wager that the cost of maintaining those ancient CF-18s is pretty high now too though.
The F-15EX isn't a particularly survivable aircraft on its own. It is a plane you'd only use if you have stealth jets and you plan to do air combat at scale. It augments the capabilities of something like an F-35 but isn't something you'd add to your fleet unless you had a lot of stealth aircraft.
Canada could very well operate the F-15EX without a fleet of stealth fighters. The F-35 is not an interceptor platform in any sense of the word, in an "all out" scenario like you're suggesting it's doubtful they would be any better than the CF-18 they have today.
The modern F-18's and the new F-15's would have also made sense, but agreed that modern F-16s would seem to be a nearly perfect fit if a single engine is now deemed acceptable. Given we like to keep equipment for as long as physically possible (and then some), the F-35 might have more runway (rimshot) in that regard though.