The worst idea was definately AGA. More resources should have been put into making AAA available when AGA came out. The A3000+ should have been the A4000. A4000 was filled with poor choices and feels like it was rushed out. For one, the loss of the flicker-fixer were just idoitic. When I upgraded from my A3000 to an A4000, I was so upset that my newer computer couldn't use the nice monitor I was using on my A3000 and I had to spend all this extra money on an expensive 1942 monitor.
The decision to put a HD floppy in the A4000 was good the fact the drive was 1.5 height left you with a completely useless 0.5 height drive bay. But to make matters worse, since the A1200 didn't come with an HD drive, no commercial developers used HD floppys. This left the HD drive in A4000s useless except for personal purposes and game were coming on 14+ DD floppies instead of a more reasonable 7.
Also the A1200 should have come with an 68030 as standard (or a 44 or 50Mhz 020). 25Mhz 020's were too slow in comparison to standard PC's and Macs of that time.
But really, I think the biggest problem was that ECS was just too good and AGA was not enough of an improvement. Developers mostly just targetted ECS machines as that market was bigger and as a result there was not enough incentive for many people to upgrade to an AGA machine. ECS thrived for much longer than it should have and AGA machines never sold as well as they needed too.