For instance, it is impossible to read a Wikipedia article on complex issue because one needs to follow a link which is not saved in PDF.
I need all links to be pre-downloaded for offline reading.
This is what I do. I have the Pages App on my iPad. I copy and paste anything into it that I want to continue to read, reference or check it out later on. I only use this app for this purpose. I also created a reading list on Quora too, but I've only just started using this feature. If there is a specific app for this, let me know, I'd use it.