I would love it if the automap could display kills / items / secrets. As it is now, you can see this information only if you use the alternative HUD while playing.
I also find it much harder to secret hunt with eternity than with other engines; using Automap nor IDDT doesn't seem to reveal secret locations very well.
I love the engine by the way, thanks to the developers for their hard work!
Edit:
Here is another one: the option "Novert Emulation" has to be turned "on" for me in order to disable mousespring, aka, disable moving forward by moving the mouse forward. The meaning behind this option isn't clear at all to me, and also, as a default should be set to on since I would guess that the majority of people don't play with mousespring.