If your primary purpose for the iPad is reading PDFs then the choice is quite clearcut get the retina iPad.
However if you're going to be doing a lot of research i.e multiple open PDFs, taking a lot of notes, writing papers while referring to those PDFs and so on, then I'd caution that there really is a huge difference between an iPad and a laptop for those tasks. I'd suggest considering an ultrabook with a higher resolution display or the Macbook Pro with Retina display.
If I could afford a Macbook Pro that'd be fine, that's way out of my budget though (I'm going to have like $650 to spend on a laptop or tablet max) and being able to hold a tablet to read seems really nice to me, as well as being able to use it in portrait mode. I'm aware of the iPads limitations, but having messed with one I think apps like GoodReader and the new multi-tasking gestures will get me through. It'd be nice to be able to have two apps open side by side, but for my budget the quality, battery life, and portability outweigh that for me personally.
Anyway, I'm doing work with a group and we have a shared Google Docs account that we upload relevant articles to, and I logged into my Google account at the Apple Store and honestly I didn't think the difference was mindblowing. The new iPad looked better I guess, but for some reason text on the PDFs looked really soft. I'm not sure if it was because they had been scaled down in resolution when they were saved to Docs or what, but I didn't like the look.
The 2 on the other hand was noticeably not as sharp, but still readable at full screen zoom.
That's been what I've kind of been asking myself, whether or not I really
need the Retina screen. I went to a few sites with pretty small text (Wired was the main one I used) and while the Retina screen is very nice, everything was perfectly legible on the 2.
At this point that's been making it easier to convince myself to get the 2 because I was already iffy on the battery life/ charging time issue and the heat. If those aren't as big a deal as I'm thinking I might go with the new iPad though... like I said, I'm sure I'll be happy with whatever I get, I just need to pull the trigger and get it over with.