Because exploiting bad AI is not a particularly worthwhile game, and the developers haven't brought the AI to a level where it can play the game or understand what players are doing; plus, the game was designed to exploit bad AI, which is just bad game design.
Academy spam would be far less effective if the AI played the way a human player would and actually try to win, and is overrated even in SP - much moreso in RT with the increase in build time, but even in the base game the results are not significantly better with Academies than without, and if going that route I'd rather use a different path than the "correct" one you try to browbeat everyone into using every game.
Part of the problem is that the way trade routes are designed makes them nonsensical, and constant micromanagement is necessary to optimize them. Nonsensical and just plain bad game design is a large barrier for the AI playing a fundamentally broken game, and sadly Firaxis doesn't put effort into fixing fundamentally broken things. And of course, 1UPT destroys the game, whether with AI or human players, because 1UPT is dumb.
re: what affinities are "supposed" to do; I don't see any reason why Harmony players have to love the planet or the bugs on it. If you're close to bugs and need to kill them, then I'd kill them no matter how planet-conscious I am. I suppose the biggest contrast is that Supremacy and Purity aren't strong enough at countering the bugs, and there is too much to gain from killing bugs rather than making peace with them. If Harmony had some bonuses for maintaining good relations with the native life then it would give Harmony players incentive to do so, without forcing them into a narrow path of saving the termites.
Quest rewards are suppposed to be a significant source of affinity and guide affinity path by something besides tech, but they're way too random and too easy to fulfill.
What use is there for extra culture? After the +3 expeditions and +30 science for explorers, I don't really need any other virtue.
There's a wide wide tree to pick from.
It's sad really. BE tries to use some subtlety in its design and got it fairly right at points, but the fan base considers that the problem; but BE also has so many fundamentally broken things like 1UPT that the fan base goes out of their way to defend. I wish RT spent time fixing the things that were broken instead of patching over broken systems with more broken systems. Until Firaxis releases a patch to implement useful MUPT I can't bother with the game, but that would be the start to making BE worthwhile as a strategy game.