I've been working on a Zend Framework application which currently does a bunch of things through Zend Application and a few resource plugins written for it.
However, looking at this codebase now, it seems to me that using Zend_Application just makes things more complicated; and a plain, more "traditional" bootstrap file would do a better job of being transparent. This is even more the case because the individual components of Zend -- Zend_Controller, Zend_Navigation, etc. -- don't reference Zend_Application at all. Therefore they do things like "Well just call setRoute and be on your way," and the user is left scratching their head as to how to implement that in terms of the application.ini configuration file.
This is not to say that one can't figure out what's going on by doing spelunking through the ZF source code. My problem with that approach is that it's to easy to depend on something that's an implementation detail, rather than a contract, and that all it seems to do is add an extra layer of indirection that one must wade through to understand an application.
I look at pre ZF 1.8 example code, before Zend_Application existed, and everywhere I see plain bootstrap files that setup the MVC framework and get on their way. The code is clear and easy to understand, even if it is a bit repetitive. I like the DRY concept that Application gets you, but particularly when I'm assuming first people looking at the app's code aren't really familiar with Zend at all, I'm considering blowing away any dependence I have on Zend_Application and returning to a traditional bootstrap file.
Now, my concern here is that I don't have much experience doing this, and I don't want to get rid of Zend_Application if it does something particularly important of which I am unaware, or something of that nature. Is there a really good reason I should keep it around?