I don't know how CU factors crash testing. The "recent issues" are,
AFAIK, on one test that the II has just started using. Maybe that isn't (yet?) a big enough issue to affect ratings.
I'm sure recalls factor in, but long-term reliability is probably a much larger factor. Toyota has built up a very strong long-term record. Even if Hyundai's 2012 models are every bit as well-constructed, there is no real proof of that yet, it will take years to establish a long-term record. Ditto Ford, etc.
The global auto market is becoming more competitive, formerly peripheral brands like Kia are making good cars, Detroit is fixing its reliability and design weaknesses, Toyota is staying conservative which may give everyone else a chance to pass them. In 5 years, will Toyotas still dominate CU's list? My personal bet is "no", I think they wil be well represented but no longer so strong.
But I think you will still be puzzled about why cars you consider"boring" are still topping CU's recommendations.