Just a few thoughts re: Workflow and UI.
I think it's a matter of learning the intended workflow of a program and taking advantage of its strengths. This would be more effective than trying to use the program as if it was a different program. My background is design, animation and visual fx for live action features and commercials and, more recently, television animation, and I've had to learn many dozens of programs over the last two decades+. I sometimes find it easier to learn new programs by pretending I don't know other programs because otherwise I might get hung up on some familiar workflow detail, only to learn much later there is actually an easier and maybe better way to do what I want in that program.
I don't use Flash, but at my workplace, we typically use Moho, Harmony and After Effects for 2D character animation, usually in combination. This is because each program has its own strengths and weaknesses, but together they compliment each other. For example, After Effects excels at compositing and fx work but is weak for character animation (even with DuIK, which we also use), Harmony excels at frame by frame animation but it's a bit clunky for rigged animation and fx work, and Moho's greatest strength is its excellent bones, IK, and Actions animation systems, but it can be a little weak for visual fx. But by leveraging the strengths of each program, we can animate almost anything very quickly, while maintaining high quality standards. The price, however, can be a steep learning curve since all three programs work very differently from each other.
Fortunately, Moho does work enough like After Effects to make it easier to learn. Just don't expect it to behave
exactly like AE or you'll find yourself getting frustrated. It sounds like you don't like Moho's layer panel but there are actually many advantages in Moho's layer system over AE's. For example, Moho's Groups and AE's Precomps may seem analogous but in Moho you can animate elements for all groups in the same window, but in AE you're forced to animate elements for each precomp in individual windows. This disconnect with AE can make it awkward to animate multiple characters with. In Moho there are also many ways to access and filter layers that's not possible with AE, using various shortcuts, modifiers, SmartBones, Tags, and the new Switch Selection window. In my experience, animating characters with hundreds of layers can be so much easier in Moho than it is in AE--you just have to know the tools and know when to use them.
I'm just advising that, even though aspects of Moho will seem familiar coming from a Flash/AE background, the best approach is to keep an open mind about the program when learning it. After you learn the basics, and you still have questions, these forums can be an excellent resource for answers you can't find in the manuals.
Also, to say you have no need for the bones/IK system in Moho does sound a bit odd since many animators feel it's the main reason to use this program. You should definitely give it a chance.
I hope you'll stick around. Good luck and have fun!