The honest answer is: I have no clue. Zug has never documented any of his changes, nor left any comments in the code. So I, for one, don't know how to answer that question.
What we do know, is that we've updated to an eAthena that is nearly 1000 revisions later. Granted, not all of those revisions may have applied to us, but I think its safe to say that we've probably fixed a dozen or so small bugs. That being said, its probably fair to say that we've probably incurred a dozen more new ones as well.
Here is a tiny list of the top-most questions that I've been asked -- and hopefully an adequate answer to many of them:
Q. Is homunculus implemented?
A. Yes, homunculus are implemented in our build of eAthena -- however, we have chosen to keep them disabled until we can fully test them. We have a few issues with the way they are implemented; so please be patient as we work through those issues.
Q. Is Rachel implemented?
A. There is a good deal of code already written for Rachel, but we are still missing proper NPCs. If you have a copy, or are interested in making these NPCs, let me know.
Q. What happened to @autotrade?
A. As per our poll, autotrade has been disabled until further notice.
Q. What happened to the bank NPC in Prontera?
A. It should be right where it used to be; after I moved it this morning.
Q. Where did the PVP NPCs go?
A. We have defaulted back to a kRO version of the PVP script (mainly because I was lazy to fix/import it). If you really want to see the old PVP script, let us know.
Q. I heard there was a new client released?
A. Yes, please go to our download site on our webpage for details.
Q. Are Ninjas implemented?
A. No, they are currently disabled until further testing and verification is done.