Yeah, no facts here, sorry, but consider this: If Gateway really didn't want to do anything with the Amiga when they bought it, why did they not only reestablish Amiga Technologies GmbH as Amiga International, but also create the Amiga, Inc. US subsidiary? OS3.5 was also released on their watch. The fact that things came to such an immediate halt in late 1999 (especially after sinking all that cash into R&D for the MCC) suggests that something happened very abruptly.
Threat from the Redmond Beast? Who knows, but even without direct interference from Microsoft, I do think the stranglehold that Windows has had on the market since the late 90s has made it harder for the Amiga to regain a foothold even so far as to product recognition, if not sales. Remember that many 1200s and some 4000Ts were still available at this time, so the supply/availability problems we have now weren't an issue. It was also before phase5 blew up, so plenty of accelerators were around, too.
I think the reason this is interesting is because I seem to recall that Gateway didn't sell the Amiga to Amiga, Inc. (nee Amino), but granted them a very liberal license. Thus, it seems like the possibility may exist for Gateway to come in, cancel Amiga, Inc.'s contract and clean up this whole mess we're in now. Gateway's market position is a lot weaker than it was a decade ago, so if they're smart, they'll consider picking the Amiga back up as another potential revenue source (wishful thinking, yes). Even if Microsoft does threaten them (more difficult now that the US Antitrust lawsuit has sort of concluded), with PC hardware prices falling by the day, even bundling a non-OEM version of Windows with their regular systems probably wouldn't affect the cost too much.