In flashDevelop your dealing with code so there's nothing visual when your in the program its just code. Its aimed towards just programmers and not artists and animators.
In cs4 however you have many drawing options to create your graphics and you can place them in your game from within cs4. You can draw and animate your characters which is not possible in flash develop.
So really it come down to whether your into just coding or creating the graphics and animations for your game as well.
Is it still possible to create acceptable animations using FlashDevelop?
If by acceptable you mean the ease of timeline animations, then no. What you can do though is use the movieclip.graphics methods a lot, or use an external program to create visuals and then go on from there - with something like tweenlite or your own custom code.
The thing Flash CS4 completely lacks, and which is mildly supported in FlashDevelop, is refactoring - which means a lot less time you have to spend going through every line of your code. Also, code hinting might seem okay in flash, but once you've tried FlashDevelop or FDT, it immediately becomes clear it sucks - big time. Flash has no support whatsoever for code hinting with custom classes. Also, compiling with the Flash IDE is a slow and tedious process - I know of a project I've worked on that took 6 minutes to compile with flash, versus only 30 seconds with fcsh - a command line compiler used by both FlashDevelop and FDT. And I imagine the time difference only heightens with bigger projects.
But yeah... for beginners, Flash CS4 is the best thing to do, unless you already understand at least the basics of programming.
Hmm. I would say that it's a lot easier to make something in CS4, and the layout is easier. You could make the quality the same, but it would be incredible hard and time consuming.
Does CS4 increase the overall quality of the project, or does it just increase the speed of making the project?
If your new to flash and Actionscrip then you will find flashDevelop very daunting, So the speed of the project will be slower. However if your familiar to actionscript then it will be almost as fast and good as CS4.
I think all code also makes the game run slower if you have more code but I'm not totally sure.
Flash develop isn't all code its just that you cant create, view or edit them within the program. Cs4 automatically codes in the graphics on the stage but in flashDevelop you have to your it yourself. There's the same amount of code really so I don't think it would make it any slower.