Bashiok has finally revealed the reasons Diablo II patch 1.13 was delayed.  Basically, the Diablo II team resources were moved to work on an emergency contingency when the Warcraft III custom map exploit affected players with injected malware.  This is what Karune said on January 5, 2009:

Blizzard Quote:
Warcraft III Custom Map Security Warning
We have identified an exploit that could allow malicious software to be spread through Warcraft III maps. We have applied a temporary fix to address this issue when playing on Battle.net, and we are working on a patch to permanently address the issue when playing on a LAN or playing single-player custom maps.

In the meantime, we recommend that players avoid downloading maps from unofficial sources or websites they do not trust—be aware that corrupted maps may share the same name as other popular maps. If you encounter custom maps that no longer function or other issues related to this fix, please post details below.

As a reminder, this is a serious issue we are working on, and we want to make Battle.net the best online service for gaming as possible. Please only post in this thread if you have constructive feedback to add in regards to this Warcraft III exploit.

This was obviously a very critical exploit that needed action.  The Diablo II team really wanted to dispatch patch 1.13 to players back then, but reality-check things happen.  The good news is that the patch to fix Warcraft III custom map vulnerabilities is now on PTR. Once that PTR is over, the Diablo II team will be free to resume work on the final steps of Diablo II patch 1.13.  They were almost ready to launch within a two-week window.  That means patch 1.13 will be hitting PTR any time in the next few weeks folks.

We want all our fans and visitors to be alert on the news and to join Diablo II patch 1.13 PTR to submit feedback and bug reports to the developers.

You can read Bashiok’s long story after the break.

Blizzard Quote:
Many of you are wondering what’s up with the patch and the ladder reset. While I’ve sprinkled some information around, it’s about time it was all mashed up in one easy-to-read location.

The Story –
Once upon a time our internal legacy development teams wanted to put some much needed love into Diablo II. Diablo II doesn’t have tournaments with millions of dollars swirling about them, so it generally took a back seat to the patch development time of our other legacy titles. But one day the planets aligned, and it was finally time to give the old girl a new coat of paint and break a bottle of champagne over her bow with the release of a patch. This went well. Meetings were held, the community was involved and polled, and an extremely long list of ideas and changes was created. That list was then cut down to changes felt to be either necessary changes, or easily implemented to ensure development time was efficient. This also went well.

Not long after, the alarm bells sounded. The patch was progressing quickly, and the release was potentially imminent. Early on it was decided, and somewhat of a no-brainer, that a ladder reset with coincide with the patch release. With the patch progressing well, a potential release of two weeks was estimated, and as always this is the exact amount of forewarning given to players and the community before a ladder reset. An announcement was made quickly and immediately to ensure a full two week notice was given. There are many reasons for this standard two-week notice, not the least of which is that most players don’t understand the meaning of ladder and non-ladder, and how a reset affects their characters. Following any reset our support departments are flooded with issues related to the change of their characters, so we attempt to inform beforehand and avoid any unnecessary confusion.

This was all well and good, the community was excited, and the developers were having fun and enjoying being able to work on Diablo II again. Then, as it tends to do, reality struck. (Warcraft III Custom Map Security Warning https://forums.battle.net/thread.html?topicId=16888549346&sid=3000) Work had to be swiftly and immediately realigned and has and continues to be focused on addressing issues for a different title to resolve a very serious issue.

The Now –
The Warcraft III patch is now on the Public Test Realm (PTR) and testing is progressing. Once that patch is released work can shift back to Diablo II and the 1.13 patch, and we’ll be working to getting that patch up on its own PTR as soon as possible. This could be a matter of weeks. Once it’s up and in a testing state for all of you, it’s then going to be a matter of ensuring the features are good and it’s a solid patch. The more people we have testing the patch and providing valid feedback, the better the patch will be, and hopefully the quicker it will be released. So that’s my challenge to you. You’ve been waiting a long time, you want an awesome patch, you want a reset. To get all that, we need good solid testing and feedback, reproduction steps for bugs, detailed descriptions of issues or errors, etc. So once this goes live on the PTR, I expect some crazed-youruinedtheeconomy-testing.