In the long run this might not be so bad:

1) Most of the waste heat is generated away from the HU. With a non-monsoon stock HU, I still have heat problems on long family drives. After 3 hours or so we have to go music-less for a while so that everything can cool off. (This is with the empeg below the HU).
2) The SQ from the monsoon should be the same as the non-monsoon stock HU or better. Certainly acceptable for the majority of people.
3) Hopefully more car manufacturers will start competing by providing separate amps as standard. They will probably get it right and provide an amp with standard line inputs and amp-turn on control, which in turn will hopefully galvanise VW to "Get It Right(tm)" too.
4) If every VW has monsoon, there will be a larger market for an aftermarket pre-amp to drive these things properly, hopefully enticing one of the aftermarket suppliers to oblige.
5) To use the non-monsoon stock HU you still need to buy a Blitzsafe adapter to allow you to use the CD input. This is about $70 anyway. And you still have the heat issues.
6) You can use that Blitzsafe adapter with monsoon HUs anyway. With the current lack of tuners for the empeg, this is a solution that shouldn't be overlooked. And you shouldn't suffer any heat issues.

Don't get me wrong. Would I rather see VW provide a standard amp? Yes. With a proper remote-amp turn on control? Of course. Is this likely to happen anytime soon? I doubt it.

But this standardisation to the monsoon system may have long-tem benefits for us VW drivers. I'm going to have to deal with their ICE solutions one way or the other, as I enjoy the rest of the car way too much for that to put me off buying a VW.