This is a really pointless thread, as everyone has their own separate ideas about what should and should not have been done by Commodore, but I might as well throw my own 2 cents in the pot.
1. Worst idea was selling the Amiga to any company in the first place and losing control of the company's future. I know that this is all unrealistic, but I wish Jay Miner and the group of great hardware and software people he had gathered together to create the Amiga could have somehow kept a controlling interest in the Amiga and just sold enough minor silent partnerships to make it into production. I believe that Jay and company would have done a much better job of staying ahead of the competition and doubt that they could have done any worse at marketing the Amiga than Commodore did.
I think Jay & company might have given us ECS and AmigaOS2.0 within 18 to 24 months after the initial release of the A1000. Although all Amigas would have retained the ability to display 15khz modes for compatibility with TV monitors, all models after the A1000 would have included flicker fixers and starting with the A3000, the OS would have the option of running in RTG mode. Video card drivers would be developed by every video card maker because by the time the A3000 was released the Amiga would have been so popular that it would have been competing head to head with the Intel PC compatible computers and Apple Macs because of number 2 below.
2. Second worse mistake that Commodore made with the Amiga was to allow the misconception that the Amiga was only a games machine to persist. Commodore should have either subsidized the creation of business applications, or developed them "In House". Money spent in this way would have made much more sense than wasting money on creating the A2000 with ISA slots and developing crappy bridge boards to allow Amigas to run MS-DOS, or Windows3.1 apps. Having better apps written natively for the AmigaOS which could run circles around any Intel PC clones that were available when the A1000 was first released would have made a much better impression and shown how superior the Amiga was in comparison to the PC or Mac. With the Amiga's hardware advantage at the time of it's first release, it should have blown away all of it's competition in every part of the software spectrum, including business software for the PC and music and desk top publishing on the Mac. By default of it's superior hardware capabilities, game designers/programmers chose to write games for the Amiga with no incentives from Commodore, but business application programmers of that time did not see the need for any of the Amiga's sound or color advantages and since Commodore had made no, or little effort to market the Amiga to businesses and corporations, there was not sufficient incentive for business app programmers to write their apps, or port their apps to the Amiga.
3. With the Amiga's huge advantages in creativity potential, Commodore should have pushed them into every school on the planet, just like Apple did, or attempted to do when they were getting started. Had Commodore beat Apple into the schools, it would have made a huge difference in what parents and kids themselves would have purchased while they were in school and after they got out of school. It also would have fueled the creative minds of millions of kids to create wonderful programs and computer generated music and art on those Amigas for everyone to see and listen to which would have been better advertising than anything Commodore ever did on TV or on the radio.
Hind sight always seems better and easier, but nobody really knows how things might have turned out if this or that had been done differently in the past.
As for those that list one Amiga model or another as one of the three worst Amiga ideas in history, I would have to disagree. Their timing may have been bad, or way too little way too late, but I can enjoy any of the Amiga models and would not call any of them completely useless, or crap. I rather like the CDTV's looks and it could have been a great idea if it had been marketed correctly at the right time. Of course coming after the A1000 it should have had more advanced capabilities too, not just the addition of a CD drive. The A600 is a nice little machine, if it could have been produced and sold for a very low price just for gaming, but it's lack of expandability and late release with virtually the same capabilities of the A1000 and A500 did not make sense.