User Agent strings are an archaic form of identity. In the case of Microsoft, much of the web tries to put IE off in its own corner due to its history of incompatibilities. The general answer has been to detect "MS" or "MSIE" and throw it a less capable site, or even worse, simply refuse to serve a functional site.

If Microsoft want's IE11 to be taken seriously, I think they've played their cards properly, as this should bypass existing IE filters. It somewhat feels like "deception" (Microsoft trying to fool the Web), but in their defense, the IE filters out there are not discerning enough -- somebody couldn't get their site to work in IE8, so they blocked ALL IE. There's no way Microsoft can combat this other than this tactic.

Now, if IE11 fails to deliver, I think they will only make the situation worse, as people will start building Trident filters.