I know this is subjective but it seems like the iBook store is really limited across nearly all categories. I know we can use the kindle app but I prefer to use the iBook app.
I agree completely. I prefer the iBooks interface much better than the Kindle App, but alas, Kindle has a fantastic amount of content. So I've been using the Kindle App.
Overall, Kindle is a nice experience, but I just prefer iBooks.
Its going to take time for them to build up the catalog. Remember when Apple first introduced TV Shows and Movies the selection was very limited for a while.