I dunno which version of android you are talking about (I am assuming jelly bean) but I think the problem is that your phone thinks that there are a lot of apps which open ebooks.
so basically you have to set default readers by file type:
i.e. epub - aldiko
to do this when the choice comes (assuming you are opening an epub file)
just check always open choice before clicking on aldiko ....
but this means that it wont ask you next time and all epubs will be opened by aldiko ...
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