Just a preference really I guess.
To my understanding the counter displays how many page turns you have left with the current charge, or rather, counts down from 9999 and you can then kind of approximate how many turns you have left from experience and use of your Reader.
Having the counter by the page numbers would just drive me batty, I mostly only look at the page number on the bottom bar, looking at the other things only when needed. Such as the clock and the battery bar.
I feel this counter goes in the "as needed" box. Where the page number is more of a readily needed thing.
If you can understand what I'm trying to say
Paperbooks have page numbers, not clocks, pages left counters and battery bars :P So I like those things to be less in my face
Which they are right now, but the counter in it's current position kind of distracts me from my reading experience.
Here is a quick photoshop to make it a little more clear what I'm talking about.
Clock isn't shown here, but it was just a quick hack and slash of a google image I found.