Interesting question but ruined by the line:
"If Commodore and the Amiga had survived and thrived"
makes it much harder to answer. The Amiga did well for 6-7 years despite Commodore, not because of it, and I believe that Amiga would have had a much better chance to thrive without Commodore. That said, the last chance (and a slim one at that) Amiga had to have a life after Commodore was back in 1995 when the Commodore UK management buyout failed and Commodore's assets went to Escom, who themselves imploded not much after. With a good management, a bunch of fore-site and a massive amount of luck the Amiga could have lived on in a more meaningful way. Just off the top of my head, they could have open sourced the OS and harnessed the community to port it to ARM. They could have licensed hardware designed out to third parties to bring out low-cost machines, it had the potential to be the raspberry pi of it's day.
I'm seeing a real lack of imagination in answering such a hypothetical question, not to mention a lack of understanding of the Amiga. For that matter, there is a massive mis-understanding of Commodores strengths as well. Commodores main strength was driving down the cost of their machines, quite frequently they out-innovated their competitors by producing machines that used fewer chips and were cheaper to produce. Before they went belly-up they were apparently in negotiations with motorola to see if they could licence the 68k chips so they could integrate an amiga chipset directly onto the chip, which would have given us a functioning APU back in the 90's.
Sure, the original Amiga relied very much on it's custom chips, but, contrary to a lot of people notions, it was always possible to write software that used the OS libraries and didn't program the hardware directly. Such software would have been immune to the hardware upgrades that the Amiga would have required over time. With the AGA upgrade to the Amiga chipset Commodore no longer released all the documentation for the hardware and forced programmers to use the OS libraries in order to use the new features of the chipset. Newer upgrades to the chipset could have advanced this idea even further until eventually the point would have been reached where the original chipset could have been emulated in software to run the older non OS-friendly programs.
Another thing people always bring up is the piracy problem. A CD-based Amiga wouldn't have had such a problem (at least until CD copiers became more common, i.e. the late 90's), and Commodore tried to bring out a CD based machine, the CDTV, unfortunately nobody at commodore had the vision to bring out a home computer with a CD drive (until the CD32 years later) and instead we got a piece of hifi equipment, what were they smoking?
Back to the question at hand, for Commodore to have survived just the 90's their management team would have to have been replaced wholesale in the mid to late 80's. Then they would have to make some far reaching decisions that would have looked almost insane at the time. In particular they would have to have dropped their line of PC clones (which is where they made their massive losses in the mid 90's), or at least just licensed out their name for another company to badge. Management would have then had all engineering focus on the Amiga (and not stupid side tracks like the C64GS, wtf) and producing a new chipset for release in CD-based computer (not hifi) in 1990. This chipset would have to have been more advanced than AGA (and released more than 2 years earlier) and probably using VRAM so that it could drive VGA monitors as well as TV's. And the machine they produced would have to have gotten over their famous penny pinching that hobbled the Amiga 1200 (SD floppy (not HD), no Fast ram and slow 14Mhz cpu when a 28Mhz chip was just a few more $'s). Then to get people developing on such a machine they needed to give away a decent development environment instead of charging a small fortune for just the documentation. For a final pice of fantasy, if Commodore had open-sourced and given away its hypertext system "Amigaguide" back in 1990....