I won't really vote for Doom and Quake, they were PC games when they first came out. I remember when the programmers of Doom said that the Amiga just didn't have enough power to run doom. This was one of the biggest nails in the coffin of the Amiga.
IMHO the biggest nail in the Amiga's coffin was piracy. Although it cost games publishers much more to produce a console cart, it was pretty much guaranteed that they'd get a return on each one. Okay, there was some limited scale console piracy, but with the Amiga (and ST for that matter), it was only a matter of time before a game was cracked and ten copies distributed to every one sold.
Not surprisingly, the game industry went the route of the console to protect their investment. That said, how they could justify a sticker price of £24.99 when the 8-bit equivilents sold for only £8.99 probably made the problem much worse.
As for Doom, Quake etc, I do remember ID software saying that they couldn't be done on the Amiga..... But to ignore these titles because they were PC ports would be unfair to those who worked hard to bring us their own third party patches - released at no cost to the end user- so that we could enjoy these great games.
:-)