Even vector-based layers are pixelated. Why?

The files I am creating in photoshop are all coming out very pixelated lately. Especially after I flatten the image or export it to a pdf. This is true even for text layers, eps files I placed, and vector-based objects I drew. The photo layers are pixelated too, even though they were hi-res to begin with and I only made them smaller when I added them to my document. Any idea why everything is so pixelated? I tried changing the file from 72 to 300 pixels/inch, but that didn't clarify the images. It just smoothed the edges a bit.

As Chris pointed out if you flatten you no longer have any vector graphics,  To save your vector graphics you need to save in a layered format. PSB, PSD or Tiff.
You can additionally save different sized non layered image files from your layered document.   When you use Image Size to resample you document to a different size vector layers like shapes and text will be resized using vector graphics and pixel layers will be interpolated using the method you set in the image size dialog or your Photoshop preferences interpolation method.  It would be best if you use a tool like one of the Image Processor scripts to save these files from your Layer documents files so your layered files are not changed and over written. Some of the Image Processor scripts use Photoshop plug-in Fit Image to do the resizing.  Fit Image uses interpolation method bicubic. The newer Image Processor Pro can be downloaded from Russell Browns web site once installed you will find it under menu File>Automate>Image Processor Pro.  Its let you set which interpolations methods should be used for different output file sets.

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