I'm sure Jay would have been very interested in the 386, it was a pretty cool CPU for it's time... Frankly had the x86 line be 32bit (with a flat memory model) when the Amiga was being developed, I expect the intel chips would have been chosen over the Motorola ones.
The 386 wasn't
that advanced - it still had a tiny register file, for example, they just kicked the registers up to 32 bits. (AFAIK you couldn't even address the "high half" as a separate register the way you could with the high/low 8 bits on the 8086/286.) It didn't even have any L1 cache. About the only really nice feature was the move to a flat memory model with an integrated MMU, and the removal of constraints on which registers could do what operations.
Whereas the 68000 had flat 32-bit addressing from day one, in addition to a large register file (which was more orthogonal than the 386's from the start) and extensive, flexible addressing modes, and by 1985 the 68020 was already out at speeds comparable to the 386 and with onboard cache, so there was a clear upgrade path (although Commodore certainly took their sweet time about exploiting it.)
And, as spirantho noted, when the 386 came out it was a pricey, high-end server/minicomputer CPU. It didn't even become common in PCs until the late '80s.
