3. Stayed with 68K.
Really? 68K was reasonably competitive to x86 during the time Commodore was around. Apple didn't move to PowerPC until 94. There were high end workstations on RISC architectures at the time, but those were largely competing for a different market than Commodore was in. The cost of an architecture switch would have been high and Commodore had made too many mistakes already to survive long enough to gain any benefit IMHO.
My top 3:
1. Not investing in the necessary R&D to stay ahead. When the A1000 was released in 1985, it was superior to the IBM compatibles and Macs that were available at the time. The A2000 had an edge over the Mac II in some respects (namely hardware acceleration), but had a much slower CPU. Later on, AGA was both too late and too limited to compete as others have already pointed out.
2. Trying to compete directly with the game consoles. A blitter makes sense for a personal computer, but the tile-based hardware common in game consoles of the time generally produced better results at lower cost. Combine this with the pricing advantages that charging developers licensing fees brings and this clearly wasn't going to work out. Further, the attempts solidified the perception that the Amiga was merely a gaming machine.
3. Not doing more to pursue "professional" markets. Apple survived because of their dominance in the desktop publishing market. The Amiga did well in video production, but that alone wasn't enough (I imagine desktop publishing was a much larger market at the time, lots of companies had internal art departments for print. I can't imagine too many did video production internally).