It's not that the ending is "bad", it's that there simply isn't enough organ. Period. For the most part, the percussion are very good (bells; tam-tams); But where the chorus sings "aufverstehen" in unison at fortissimo, the organ is supposed to be fortissmo underneath them. Mahler even writes "volles werke" (the complete works). I think it sounds stupid to have 300 people shouting "rise", with no organ supporting them. Compare this very same spot to the one on the badly maligned Eschenbenbach/Phlly M2 - or any number of other fine recordings (including the 40 year old Klemperer one) - and you'll hear a world of difference. The dvd of Boulez doing M2 in Berlin addresses this issue much better.
My only other major complaint about the Boulez/DG M2, is that the scherzo is a bit too fleet, and there's almost nothing done with the hairpin dynamics (crescendos; decrescendos) in the woodwinds, specifically in the clarinets. As a result, there's little sense of irony, or humor even. It's just there. Again, the scherzo is much better on the dvd version from Berlin as well. I actually like Boulez's quicker-than-usual tempo for the second movement. Sorry though, I can't share your enthusiasm for the VPO's somewhat "thuddy" sounding timpani. That's greatly a matter of taste, I know.
And needless to say, the unison brass from the VPO often times sound very nice. That's a plus. But the "live" version captured on DVD sounds less "studio bound", and it addresses the very specific deficiencies mentioned above.