Actually, not that late. I think their main problem was that the environment changed around them. Besides SaaS, the whole developer ecosystem changed as well: when I look at who really won the bugtracking market, it's GitHub, who added it as a feature on code hosting.
If winning the bugtracking market was the goal, they probably would've taken VC money. You may notice that everyone who's in a position to claim that has done so (Github, Atlassian, etc).
They did learn from this, as you can see by the very different paths StackExchange and Trello are on.
Joel wrote an essay about this. [1] His basic thesis is that organic growth wins over VC when there are entrenched competitors, few network effects, and little customer lock-in. VC wins when there are wide-open markets, strong network effects, and strong customer lock-in. Stack Exchange's investment was consistent with this thesis [2].
The developer tools market changed from one with very few network effects to one with a large network effect around 2010. The drivers for these were GitHub, meetups, forums like Hacker News, and just its general growth - they made coding social. When I started programming professionally in 2000, each company basically decided on a bugtracker and version control system independently, and it didn't matter what every other company did. By 2015, most new companies just use git, they host on GitHub, and if they don't do this, they're at a strong disadvantage when recruiting & training up developers, because that's what much of the workforce uses.
Interestingly, both GitHub and Atlassian resisted taking investment for many years - GitHub was founded in 2007 and took its first investment in 2012, while Atlassian was founded in 2002 and took its first investment in 2010.
