Like many other questions on this forum, the answer can be subjective depending on the specific components in your system (receiver, pre/pro, amp, speakers, cables, etc.) and more importantly, your ears and tastes. The best and most honest answer to your question (and many other questions) can be found by trying it out and listening for yourself, and then deciding what you think.
Keep in mind that most receivers and pre/pros may not have (or have limited) bass management, time-alignment, and level adjustment for each speaker in a multi-channel configuration when using the analog inputs, as compared to what is available on the digital input.
Also, note that the Dolby encoded bitstream obviously won't be available if you connect via analog. So your player needs to handle the decoding and associated parameters. For sheer convenience (less cabling and easier speaker setup) and given minimal sonic differences and a compressed format, you might find it better to just go digital (for video). Obviously, DVD-A needs to be analog.
Technically speaking, you can consider the DACs in you receiver or pre/pro versus the ones in your player. You can also consider any A/D/A conversion that may need to take place in your receiver or pre/pro to handle any processing versus keeping the processing in the player.
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