On the E2, large memory cards won't work at all, giving a card error. At the time, the largest card available was 48 meg, and the one that shipped with the E2 was 15 meg. The largest one I have that works with my E2 is 96 meg - my 128 meg is useless.
The E3 came along a few years later, and by that time larger cards were available, so they changed the memory subsystem microcode to address more space. Also by this time the CF cards were available, so those work in adapters as well. I have not run a series of cards in my E3 yet to determine the upper card size limit, but would suspect it to be 512 MB.....
If you take a hard look at the E3 vs the E2, you'll soon come to the realization that a complete redesign had been done in an attempt to make the E3 acceptable with a wider range of professional shooters than the E2 had been. Of course, this was short-lived, since the D1 follows the E3 out the door in fairly short order.