It's a personal preference thing and it depends an what you are trying to achieve. Normally people who are doing "muscle specific" routines are trying to build mass. This allows complete concentration on that specific muscle group with a day or two off in between work outs.
People who concentrate on complete body work outs, or as you stated, alternating between upper body and lower body work outs combined with cardio are probably trying to get lean.
My suggestion is, do what works for you. Understand that gains aren't going to be immediate. Listen to your body.
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