Wow! That's a lot of frustration you're dealing with there.
Flash is an amazing tool for animation...
You should take some time to look at some video tutorials from the link below.
hehe I have to laugh because I'm experiencing the same issue in reverse--3D software is pinching my crank at the moment.
I don't have any instant fixes for you, but will offer what I can:
First off, personally I abandoned the timeline a long time ago. I don't suggest this is the 'right' way to go, just an option. I do all my animating programatically. A great reference for that are the Frieds of Ed books
1: I can't explain this, but the whole entire way flash works is completely alien to me coming from 3D animation. The way the key frames and timeline works is like trying to pilot an alien ship in some other dimension where nothing makes logical productive sense.
Yup, that's pretty common...just like learning 3D apps for the first time, it takes a little while. Once it 'clicks', it becomes very simple.
4: Playback is slow. What should be 30 fps plays back at 17 fps or less. Can I set it to "low quality" in flash itself..? It does not need to have anti aliased sprites while I'm animating.
This can be caused by a ton of things. We would need to see the file or code chunks to help troubleshoot it. Check that images do not have smoothing turned on (via a right click in the library pallette, properties...)
5: Why can't I make a simple heirarchy of objects? I have to animate a neck made of 10 pieces (and another neck, and 2 tails).
You can, but without bones, you would probably have to do it programatically. Take a look at this example:
(a mildly modifed example from the Friends of Ed boksmentioned above).
Hey Man, I've been using Flash for a long time and love it to death, but I can totally understand your gripes. They are quite valid.
As others have mentioned... its just different. It is really amazing what Flash allows you to do with just a minimal understanding of the basics. Once you start needing more advanced control... well it gets harder. Most people who start using flash just want their logo to spin... and not necessarily build a snake with joints:)
You mentioned you use Flash CS4. It allows 2 methods of tweening:
Classic Tween: All beginning and ending positions must be keyframed manually
Motion Tween: Auto keyframing similar to after effects.
From my position and long history with Flash I greatly prefer classic tweening. When I need something more advanced I use the TweenMax / lite Actionscript engine. I find the new Motion Tweens to be a real pain, and unless I'm doing 3D tweens... I avoid them completely.
Once you start doing advanced CS4 Motion Tweens you are going to be manually adding specific Property Keyframes so I really don't find them to have an advantage unless there is something super specific I need to do.
Again its a matter of preference.
As for playback performance. Totally. If I want to make anything look good I set my FPS to 45. Most banner networks have limits of 18fps which is a real struggle to make look good. On a mac especially, the control > test movie output runs much worse then the browser plugin. Also in flash cs4 the stage has a live running instance of the flash player and it really doesn't handle things all that well. It is pretty ridiculous that a simple vector animation stutters at 30fps. I'm totally with you. The good news is the Flash Player / Plugin is getting better. Back in 98 or whenever flash hit the scene, most of our computers were running at what 233mhz with video cards with 8mb of ram. Yeah, sure then 12fps may have been asking a lot. But in this age of mulicore processors, dedicated graphics, highly optimized mobile graphics cards and limitless ram...shouldn't Flash play a little better?... YES! Current gen smartphones have more juice across the board then the desktops I started out with, higher resolution too!
I'm sure your 3D experience will carry over well. I'm sure a lot of us would like to take our flash skills to 3D. In no time you will find that it really can do what you want it to. It just takes a little time and a good deal and a ton patience;)