What would you say was the main reason for thrash's low point in the 90s?

There are a few candidates that I can think of, and perhaps all of them were contributing factors. The first one is the release of Metallica's Black Album. This seemed to cause other thrash bands to try similar ventures. Megadeth did Countdown to Extinction a year later, Anthrax did The Sound of White Noise two years later, and Kreator did that weird gothic metal thing.

Death metal's rise in popularity is possible as well. The same people who bought Hell Awaits in 1985 seeking the most extreme band out there now had this completely new genre to latch onto. Scream Bloody Gore in '87, Altars in '89, Effigy in '91, so on and so forth. This would make the thrash bands seem outdated in comparison. Understandable lyrics, no blast beats? Might as well throw on Frank Sinatra, right?

I would guess both points had their part. Thrash used to be the gritty underground thing that gave the elderly heart attacks, then those bands tried to be mainstream, so the seasoned metalheads went out and bought Morbid Angel and Deicide records instead.