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There's a free PDF reader called Bookman that's pretty fast and optimized for large pdf files. It has all the features of the iBooks reader (including the nifty bookshelf) plus a nifty horizontal scroller at the bottom that lets you quickly scroll through the file.
You should try out an app called iRead PDF. It's a great free pdf reader that handles large documents with ease. It has a nice tabbed interface which allows you to have multiple pdfs open at the same time. You can email pdfs directly from the app and use the app for opening pdf attachments in your email. It recognizes Adobe Acrobat annotations, notes, and highlights and you can customize the toolbars.
One thing that's missing is the convenient scrubber bar that Bookman has for jumping through docs. Also, it's not fully integrated with Safari, so in order to download pdfs from the web, you need to use their built-in browser. Both don't provide an easy way to import pdfs. If you work with large pdfs a lot, I recommend investing $1 in GoodReader, which lets you import pdfs via a wireless network or usb, and can even directly access your Gmail inbox.
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