If say Uber I sound like an idiot that can't pronounce the ü.
Just.. don't. Occasional German references in English contexts are usually cringeworthy. Uber is ridiculous from this particular point of view, just because their name is absolutely useless. Unless you're trying to make the xth Nazi reference and think that German sounding bull.,.. might so the trick, please reconsider. The shop in this article at least knew then spelling and had a decent explanation. The other (HN loved) company is just... sad. I would suport the real über if they offer a way. Uber? Ridiculous, even before this article. But hey, who cares about the language you steal your laughable name from, right?
I'm pretty sure I've seen "uber" (with either spelling but pronounced in English) on the web and on IRC as early as the 1990s. It likely spread beyond the online use when the web became mainstream.
Disclaimer: German native speaker who used to spend way too much time around linguists.
And you can't mention the German "super" in 2014 without pointing out this viral marketing campaign: https://www.youtube.com/watch?v=jxVcgDMBU94 (explanation: http://www.slate.com/blogs/browbeat/2014/02/24/supergeil_ede... )
I mean, you wouldn't catch anyone on German television pronounce Zuckerberg's name as /ʦʊkɐbɛɐk/, even if it may be of German (Jewish, I presume?) origin.
PS: I think the Duden and Wiktionary are full of shit -- I've never heard anyone in Germany pronounce "Berg" with an actual "r". Maybe I'm missing some subtleties of German phonetic transcription here, but that's an /ɛɐ/ diphthong if I've ever seen one.
Similarly, as I'm currently living in Latin America, I got used to pronounce english words and names in a spanish way. At first it feels very stupid, but locals will understand you better and you don't have to suddenly switch language flow and phonology in the middle of a sentence.
As a native English speaker who can speak decent Spanish, this was a very interesting experience for me as well. Getting used to saying your own language's words with another language's accent is very instructive. Also hearing English words with a thick Spanish accent was a bit of a head trip for me - at first you don't even recognize them when spoken to you, then after a while you sort of "get" the phonetics enough that you can think of the words as sounding like that.
All in all one of the more interesting aspects of learning to speak a language competently, or alternatively, something that makes the difference between sounding like some American kid in a Spanish class and making a real effort.
I always encourage other travelers to focus on pronunciation and getting rid of ones native language accent right from the start. Not to sound more skilled than you are or to hide your origin, but it is necessary to get into the flow and rhythm of a language, which will in turn improve your listening skills and ability to adapt to different accents of that language immensely.
And in geographically widespread languages like spanish or english you have to adapt a lot. As long as you pronounce things in one major regions accent natives have few problems understanding you, even if you make a lot of grammar mistakes. On the other hand, you can have perfect grammar, but with a really thick e.g. english accent, you're sort of limited to talk to people who also speak english and are able to do that head trip.
In my opinion beeing understood is more important than beeing correct and whatever people adapt to is ok in my book. I even learned to tolerate the horrid ways north americans pronounce places in latin america. Languages change and mix all the time. For the good and the bad. I just don't care enough about uber, and I'll just stick to the way people pronounce it once I'm back to Switzerland.
I'm not saying the word shouldn't be adapted at all, quite the opposite. I'm saying "correcting" the pronunciation to the one of the original German word it is historically based on is a bit silly because the English meaning of "uber" -- while the word itself may be derived from German "über" -- is actually quite specific and entirely different.
Now that I think about it, your "Müesli" example actually backfires. In (German) German, where "Müsli" has become a generic description for nearly any mix containing oats and milk (basically what you'll find on the German Wikipedia), the original Swiss word Müesli is often used with a much narrower and more specific meaning (equivalent with the original meaning of Birchermüesli, I think).
But anyway, for consistency I demand that you refer to Apple as Apfel (or Apful, if you want to stick with the original Old High German) and Microsoft as Mikrosanft (or -sacht? Etymology is a bit harder with this one) in spoken German, too.