Apps module is a great much, however it is not smart enough yet.
It has a great potential but in my opinion few things need to change before it can be more widely adapted for site development. I know that things that I'm going to mention should each be on a separated each but first I want to discuss the big picture, since they may have already been discussed by others

1. Documentation is the still very incomplete, getting apps up and running is not that difficult however since there is no proper official documentation new developers should search the Internet and read the specifically written tutorials they may give up trying because they think that it's too time-consuming to get it working as I almost did
I still don't know the full functionality of the apps module!

2. The manifest file can be much more flexible.for example right now we have to do specifically define the download location and the version of each module even when it is not needed. It doesn't seem possible to download the latest version of dependency modules something that drush dl module_x

3. Manifest doesn't get validated properly. it does to detect misconfiguration somehow but as I said before it can be smarter. http://drupal.org/node/1502764#comment-7031506

4. The manifests bundled with apps could be automatically imported to apps module, something that features module does. There seems to be something like that but I couldn't get it to work due to the reason I mentioned in number 1

5. there has to be a way that we don't have to manually create the manifest at least not all of it and the whole process is also time-consuming since the developed apps maybe be site specific and can't be uploaded to public server. apps module is a great way for breaking the logic. We use features for these sort of things but features doesn't download the dependencies.

That's it for now :)
Tx