Custom Post Types. Are there any disadvantages/advantages in using a plugin to develop them?

I think there’s no really huge difference, you choose the tool that you feel most comfortable yourself. Plugins have the drawbacks you mentioned, and doing them from scratch can be a bit slow and tedious.

The 3rd alternative, that I find really good, is a PHP class that does all the heavy lifting for you, but is still light and easy to use, e.g. Easy-WordPress-Custom-Post-Types. This particular class does custom taxonomies and metaboxes also. Very handy. So you’ll eliminate bunch of plugins with one hit.

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