Newspaper certainly works well enough if you only have one or two animals that you're dealing with...
Drawbacks, for me... it looks trashy. I also prefer to give my animals a NICE environment to live in... if I am going to go to the trouble of making sure my BP is humid enough, and my bullsnake dry and cool enough, then I will darn well give them a nice environment to live in, too. LOL
Aside from that, I just don't the way the ink rubs off on the animal's scales. I spot-clean my enclosures once a day, and do a total changeover once a week. Now.. I only have 3 (at the moment), though at the 'peak' about three years ago, I had fifteen total. So, while I acknowledge the extra work that goes into such things as aspen or moss substrate... I don't like the newspaper.
If I absolutely do not want to use a 'normal' substrate (normal for me is aspen, or the Soft'n'Moist that my local shop carries), then I will put them on a reptile carpet. At least that way it looks nice ...
Pine shavings - too much controversy over that for my tastes. Some say it's fine, some report deaths and other problems related to it. I personally will not risk my snake's health on something that is so 'unsure'. I stay away from pine, period. I will not bed my snakes on anything that I am not 100% sure is safe for them.
Put the animal on what you feel is best, or suits your needs. Newspaper is efficient but trashy and ugly looking, 'natural' bedding is more work-involved to keep up, but looks nice, paper towels I use primarily if I suspect mites, but no other time.
(they are a great 'detector' for mites... if i suspect a case of mites, the first thign I do after I check the animal itself is rip out the substrate, throw it out, disinfect the tank and replace it with paper towels. The bright white will show any mite that lands on it.
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1 Ball Python
1 Rock Python
1 Bullsnake
5 Cats
Love 'em all ...