The Amiga 3000 was produced for a more limited market by one company. 386 motherboards/systems were produced many manufacturers for a larger, more competive market.
That´s my point. Apples user base seems huge if compared to people shopping for NG-Amigas. If they sell their Power Mac entry level box for $2500 it is easy for them to put a 6 core CPU in and redesign the case to make the fans go extra noiseless.
When the Amiga 3000 was rumored many of my friends were hoping to get one until they heared the price. They expected it to be more expensive than the $1300 Amiga 2000, but they didn´t expect more than $3000. And of course - when the A3000 was finally out (It was late) they were comparing it to OS/2 boxes - that also did have real multitasking, Truecolor VGA gfx and higher clock speeds.
I think the A3000 is one of the greatest computers ever - I own one since 1993. But not everyone shares/shared my enthusiasm. I for one wouldn´t bash the X1000 for being late and expensive.
DISCLAIMER: I live in germany and the prices in my posts are calculated with different exchange rates at different times. They might substantially differ from what you were experiencing in your part of the world.