I know exactly what you mean - I am ofcourse waiting to see what SS3 brings with it's redeign of the admin section - hopefully this will make cusomization easier.
In my expiernce most things can go into the Pages or DataObject with the use of the LiteralField, then is something still demands complete control I subclass LeftAndMain and then create a template for the left and the main - then treat as a regular page (still use ajax for most things...)
We had this need too. The quickest way was to write a plugin -- as the Pixlr one (once workinging) seemed a bit overkill, and no others appeared.
It gives you a "crop" button next to detach / delete permananetly in the Uploadify form, and loads a JCrop enabled image that's scaled to the modal when clicked.
WARNING; this has been only tested with a DataObjectManager popup under SilverStipe 2.4 and also has an issue where the browser caches the CMSThumbnail && doesn't instantly show you the cropped image for in.
I've released a simple module for improving automatic cropping in SilverStripe 3: https://github.com/jonom/silverstripe-focuspoint
Basically, when you edit an image in the CMS there is a new field that lets you select a point on the image as the focus point - i.e someone's face. Then instead of using CroppedImage in your templates you use CroppedFocusedImage, and the image is cropped with a bias towards keeping the focus point in the center of the image, rather than always cropping from the centre.
Feedback, suggestions and pull requests welcome, hope someone finds it useful :)