I’ve stopped using the fixture adapter completely since I posted this question. I work with a highly non-standard and unstable API and therefore have a number of custom adapters and serializers which weren’t being tested at all (and whose logic I ended up having to patch into the fixture adapter – bad idea).
Instead, I would recommend either taking the response mocking approach described in this thread, or if your API is fairly standard, using EAK’s api-stub (currently a bit half-baked and in the process of being replaced with an API Fixture Proxy. Either way, be prepared to write a lot of custom code to achieve what you want; testing Ember apps is like the wild west right now, especially when it comes to the data layer in acceptance tests.
Also, regardless of whether you decide to continue using the fixture adapter or not, I would recommend avoiding calling App.reset() between tests and just creating a new app instance and tearing it down with App.create()/App.destroy(). It will introduce more overhead – and slightly longer test times – but in my experience it’s better than battling with lingering app state issues. Again, see EAK’s testing setup.