To support protected memory, you need an MMU, and the base 68000 did not ship with an MMU, however the 68020 and later did. The Amiga 3000 onwards should have defaulted to MMU and had a flicker fixer and chunky graphics and 16 bit sound to really succeed. Another multiverse timeline, perhaps.
The A3000 had a ficker fixer. If you meant that the other later models should have also included it, I agree.
Regarding the MMU, the problem was/is the OS. AmigaOS uses message passing between processes extensively, and those messages often involved passing pointers to structures that the receiver expected to be able to dereference and even writ to in some cases.
I'm on record repeatedly arguing over the years that it would be possible to retrofit at least limited memory protection onto AmigaOS, but it's decidedly not something that'd be simple to do, and most likely you'd need to basically sandbox old apps and create new API's for new apps to do it properly.