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Goodreader for iPad does annotation, highlighting, re-flow, etc.
Do understand, however, that tablets without real keyboards (as opposed to virtual keyboards) are mainly for content consumption rather than content creation. A "keyboard case" is available (from many sources for cheap$) and does the job but iOS devices are not OSX Macs; even Apple's iApps (Pages, Numbers, Keynote) are awful when compared to their OSX counterparts.
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