If you root, you can bypass those issues in most cases. I have 3 apps detecting it, that I can bypass, and only the German health insurance app from TK detects it (according to the internet, it's getting past most solutions somehow). It's not something I'd recommend the average person, but for people who care enough to fiddle, it's still the best way.

I think since my first Android (HTC Desire Z/T-Mobile G2) I spent a total of 1 week on stock, never was a fan of any of them.