The only problem, issue, flaw whatever is, that people (me included) thought there won't be any change in the speaker department compared to the Air 1. Apple didn't mention it in the presentation, some reviews didn't mention it either.
Buyers were not prepared for such a change because they expected the speakers of the Air 1 in the Air 2.
From a technical perspective, the resonance is not a result of the thickness of the Air 2. The new speakers have openings on the INSIDE to use the chassis as a woofer (see the links I've posted to the teardown pics in this thread). If the speakers in the Air 2 wouldn't fire outside AND inside the chassis, the resonance would be on the Air 1 level.
Is the resonance a trade-off for better sound quality? Yes.
Was it a design decision? Yes.
Will Apple change it? Not in the Air 2.