Ipod connection vs aux connection?

[boddy 10+ year member]

I'm going to be using an alpine 9887 which supports full ipod connectivity. But I would still rather use my phone through a 3.5 jack as its just more convenient and other people can plug there stuff in too. It also means i don't have to go fishing for my ipod and putting songs on my phone is so much easier than using itunes imo.

One thing that would persuade me is the SQ, will the ipod connection have a better SQ than a standard aux connection or would it not make no difference?

Also if i did use my ipod i would use iPod iPhone 3GS 4 Charge Adapter/Converter 12V to 5V | eBay as the alpine doesn't charge them. Would this induce any noise?

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[675R 10+ year member]

USB > Aux all day long.