I'm not sure Machinarium problems stem from the Adobe toolchain. The developer says it's because they hit RAM limit with iPad 1 and load resources statically:
"The memory limitations of iPad 1 (which are somewhere around 115 MB RAM per app) are just quite challenging. You have to have it running around 80-90 to keep it stable and the app has tons of timeline animations, the sources are 1 GB, all compiled into one single SWF file + some assets. The app was originally made for PC and upgraded for tablet devices. When you start creating tablet apps from scratch it's a whole different story. The game is now made with 'no compromises' compared to the desktop version and that keeps it unique."