iPad frustration - PDFs are frustratingly frustrating

I am a technology freak. I love new gadgets and so I spent almost a $800 for my 32GB IPAD 3g.

One of the things it should help me is with getting really going with pdfs. Meaning I want one place where to store and sync all my pdfs.

But I ended up with 5 pdf reader on the ipad and none is really great. Some show promise others were not meant for it.

1) sync pdfs from somewhere to a folder structure or using multiple tags
2) all pdf apps shall have access to a single document store!!! So I can use some app that has an advantage over others for some purpose and not sync it into that app or upload

Upload of the files over some download functionality or server is ok but not if you try to come with multiple hundred documents.

pdf apps:

iBook
FastPDF
GoodReader
CloudReader

3) allow for comments, highlighting

I am still trying to figure out how to handle my library of about 2000 documents make them accessible on the ipad without having it stored remotely on some server. The problem is that some pdfs are quite large and until the document is downloaded between 1 minute to 5 minute can pass and that's definitely too long.