I have probably 100 Kindle books and perhaps 10 iBooks.
I have a Kindle and an iPad3.
For reading for a considerable length of time I much prefer the Kindle. It's not even close.
For short reading when I'm just killing time (in line, in a waiting room, etc) I like having my Kindle books on my iOS devices, especially my iPhone as it's always with me.
I don't mind reading on the iPad3 but I do find that the Kindle is far easier on the eyes over long sessions.
All fairly meaningless ....... I have yet to talk to anyone who has both and actually READS books (at least one a week) who doesn't prefer a Kindle for READING.
In bed, in the dark, I prefer my itouch Kindle app in landscape .
I read a ton of books, I use the iPad at least 90% of the time. I only use the Kindle when reading outside in the sun (which doesn't happen a lot in London ).
Get a regular kindle since you'd only need to recharge it like once a month. Too many distractions on the Kindle Fire like YouTube, Gmail, Tapatalk, sunlight, etc.
I bought the Kindle Fire earlier, and then bought the Google Nexus 7 a couple of weeks ago. Between the 2, I prefer the N7 because it is easier to hold than the KF, and I can do a lot more with the N7 (and it is blazing fast). That said, the iPad3 is still the best.