There could be a very intuitive solution to the zooming page: allow one to select a tool to crop the pdf with your stylus by tapping the (2 or 4) corners of the rectangle you would like to zoom in to -- and consequently make this the default cropping for all pages of this specific pdf. (Well, there are some considerations to be made, like when you cannot accurately view a single page or scrolling on pages is required. Then the selected area can nonetheless be considered as the only area of all pages/this page you're interested in (the rest would be the margins). It would end the hassle of fiddling about to exclude the proper margins.)
A A A A
A B B A
A B B A
A B B A
A A A A
becomes by selecting the dots (presumably after selecting a cropping tool)
A.A A A
A B B A
A B B A
A B B.A
A A A A
In this case A would be the margins and B the text.
Anyway, could you elaborate on the reading of scientific articles? I'm mostly interested in
these sort of articles -- LaTeX a4/a4-wide and journal publications. For example can you comfortably read a wholepage in full screen, with or without margins?