IMHO the problems many people have with the stock setup are caused not by the antenna being blocked by the plastic fairing, but rather by the other metal and electrical items inside the fairing that affect reception. I think I've mentioned before in one of these threads that there's a good reason why the automakers don't bury their sat antennas in the instrument panel under or near the radio chassis and metal brackets. Yes, it would be much less expensive to do it that way, but even though auto companies would normally kill for ideas that would save only a penny or two per unit they usually try not to do things they know will cause poor performance and customer complaints. Thus they still spend a lot more to locate the antenna outside of the instrument panel and usually outside the vehicle. Say what you will, but the auto industry does get some things right some of the time, and this is one of those things.
If people are having reception problems but still want to leave the antenna inside the fairing, I'd suggest moving it from the stock location to a position above any metal and as far from the audio components as possible, even if it means making your own mounting bracket or adhering it directly to the fairing with 3M mounting tape. Some of the stock locations I've seen in the past made no sense at all, other than being cheap and simple for Harley.
JMHO - Jerry