The first principle is, PDF is not a suitable format for reading books, period. Especially because, as you say, you cannot easily reflow pages and font sizes the way you wish. Whenever you can, avoid PDF and get the book in EPUB or MOBI instead. You can also easily convert other formats into EPUB in free software such as Calibre. PDF is a pesky format, so it's not easy to convert from it. I've had better results converting from PDF to EPUB/MOBI using Mobipocket Reader than Calibre. Once you have a book in EPUB, read it in Marvin.
If you absolutely cannot avoid reading a book in the PDF format, then you need the best software that there is in iOS for handling PDFs, to mitigate your suffering as you read the file, as much as possible. In my experience, the best software for handling PDFs on your iPad/iPhone is GoodReader or neu.Annotate.