I don't think it's "regrettably" that the classic GPL (v2) is featured over v3. Many, many GPL projects have decided v3 is a bad license, so newbies shouldn't be pushed in that direction.
The wording of the patent clause is broader than most of those who participated in the drafting intended, in a way that could be problematic for most companies. The GNU project themselves, the creators of GPL. v3, have had to disavow the plain language of the license, claiming it doesn't say what it does.
I think most people intended that if you release code under GPL, you give up patent rights related to the code you contribute. The wording is broader than that, though. The way GPL3 is actually worded, if a company contributes to any GPL project a third party can use that project to nullify other patents from some other division of the company, arguably. The issue hasn't been tested in court, but it's enough of a risk that many companies won't touch GPLv3 code. It could cost Apple, Samsung, or Google tens of millions of dollars if that loophole allowed competitors to nullify their patents, rather than having to cross-license them.