My 2 cents:
1 The toy-like color scheme and preferences of OSes before 2.x. The early Amigas were never taken seriously by business and corporate types the first 5 years of production. Only the TI-99's color scheme was more toy-like and hideous.
2 The strange font system. The Amiga, despite it's many strong points, is still not the best for producing documents and printing.
3 There should have been a networking solution built-in from the beginning. Hindsight is 20/20.
4 Hard drive solutions, when they appeared, were too expensive. Already said.
5 Paula should have been improved as early as possible to CD quality sound. Also, already said.
People always mention the gaming ability or the multitasking (still excellent), or video output. I still love the dynamic ram disk and RAD:. The Amiga was the first comparitively inexpensive computer that could display photographic quality images in color. The OS was beautifully engineered to be near "real-time" and extensible and it is still unique and relevant in 2010, at least to me.
