1. All those requests would be solved by user definable toolbar or dynamical (self learning toolbar with possibility to switch on/off the learning). Different people need different features at hand.
2. Good idea! And maybe add the possibility to choose the reader app for given file. Also would be great to have separate set of settings (zoom level, cropp, ....) for files when viewed landscape and portrait. It would help a lot, I think.
It would be also good to have a look on look of icons (there was a common conception, but as features were added some icons do different tasks than one would expect) and logical placement of icons. (I would make easier to use Onyx for a new user). Also many icons on toolbar of Pdf Reader are very bad visible (black on gray - they need at least white outlines). And icon on toolbar that is switched on should be well visible, now it is sort of gray. Maybe white frame arounr the button would do the job better.
I know there are more important things, but easy to comprehend interface is also important.