Make a pull request, sir.
Here is the suggested CI method for executing database queries: http://codeigniter.com/user_guide/database/examples.html
Nowadays, I prefer (PHP) frameworks with real autoloaders and better OOP usage (like Zend or Kohana).
http://www.php.net/manual/en/intro.pdo.php
In this sense, wouldn't it have been better to either recommend that he should have used a DBA library? Or even recommend that he used PDO in place of CodeIgniter's own DB access library?
The OP's experience aside, I think you're also missing that this was written on top of CodeIgniter. From my own experience and learning, CodeIgniter isn't really the best tool for writing larger applications. It's architecture isn't so great and is largely a remanent of the past. To end a rant about CodeIgniter short, it seems more natural to write namespaced procedures using classes rather than taking full advantage of objects and OO (again, probably due to it being largely a PHP4 framework).
Plus, I really disagree with his comment.
Besides, this was a personal project, probably created without the intention of eventually open sourcing it. If he only ever intended to use MySQL, and portability across RDBMS systems wasn't a goal, then it's fine as it is.
Seriously though I agree with your point about PDO. Perhaps the down-vote was due to the comment about de-engineering and apparently making fun of 10k LOC?
I took a look at the app and it's got a huge amount of features. 10k is not really that much code for a "enterprise" app I suppose you could call it. The OP probably is just trying to express the amount of labor that went into the app. Unfortunately other developers may judge your LOC as either a positive or negative, so it's probably best to avoid mentioning it (unless you've written an app in an unbelievably low number of lines).