I say this as a lifetime subscriber of Consumer Reports, Consumer Reports stopped being relevant years ago for just about everything. They were good when there was no internet, and no specialized reporting on different products. These days, they just don't measure up against most of the alternatives.
Consumer Reports uses flawed testing methodology and always has, but that used to be the only methodology available. Basically they get a single product and then test it however they think they can, then give it a score in various attributes. They don't, and can't, take into account individual variation between devices due to a single broken device. Most of their tests are highly subjective, and done in an unrepeatable fashion, based on the particular likes and dislikes of a single individual. They do not run tests over a long enough time to show long-term reliability or real world use.
Ultimately, Consumer Reports is unscientific and very subjective. Just because you hire engineers does not mean you're getting useful data and evaluating without bias. Nor does it indicate you have particular expertise and understanding of what you are reviewing in order to evaluate different products on an equal footing based on differing consumer need.
Consumer Reports does do some things right. I trust their safety ratings for vehicles (I don't know a lot of car websites that have their own crash test dummies). I trust they have accurate information about manufacturing costs and dealer costs, to help you negotiate with a car dealership (but that doesn't help you pick what model to buy, though). I trust they will properly analyze the sugar and fat contents of various ice creams (their food lab no doubt has the proper testing equipment to determine these things), and give a reasonable, if subjective, description of their tastes. I trust they'll give accurate, if simplistic, comparisons between different types of television screen technologies, camera lenses, or the difference between the three kinds of clothes washers (all of which I could find online easily enough). I will not, however, trust their individual brand or model recommendations for televisions, cameras, or washing machines in each of those categories.
For large appliances or technology purchases, and yes, even cars, I trust many different reviewers, from specific websites dedicated to discussing those products, backed up by thousands of ordinary customer experiences. I routinely see Consumer Reports getting things very, very wrong, recommending products that are universally reviled, and criticizing products for things ordinary customers don't care about or never encountered. Yes, there is self-selection bias, and only the most upset and most ecstatic customers will review a product online, but it's in those extremes you get a fairly accurate picture of what you can expect, both the good and the bad. For all the stuff in the middle, there are specialized product reviewers on specialized sites that have far more expertise in real-world use and the market as a whole.
The one thing Consumer Reports does really well is their yearly survey where they do actual, scientific, statistical analysis on a host of different product categories to determine reliability and customer satisfaction. This is the only way to do it, and Consumer Reports can tout their credentials in that. For everything else, there's specialized reviewers who know what the heck they're talking about, and the internet for long-term and real life use reviews from thousands of actual customers.
I've never found their single-test technology or appliance reviews all that insightful, in any category, and have thankfully always found much better reviews elsewhere. They're good to look at, just for brand information, but for specific models? Forget about it.
The iPhone 4 debacle was, quite simply, a desperate attempt at getting some attention to a dying business model of single expert reviews. Luckily, those days are behind us, and have been for many years. I'm sure it had very little impact, as will this new report on the 4S. I don't think they have an anti-Apple bias. They've always rated Apple products pretty highly, though they've never liked Apple's prices. This was, I'm quite certain, an editorial decision made for business and attention-seeking reasons. The bias was in wanting to get mentioned on TV and blogs a lot, and nothing more.
Consumer Reports will hopefully be around for many more years, and their own current efforts at pooling consumer data online may help them to achieve relevance again, but anyone relying solely on their reviews for information is a fool. A good starting point, yes, and a place to find a comprehensive list of models to see what's out there, but best taken with a grain of salt and always double-checked from the real experts and real consumers.
Again, this from a lifetime subscriber. Consumer Reports just isn't relevant anymore.