Concerning the ads: Do what Pablo said and write to Amazon explaining that you bought this device from a local retailer advertised as ad free and tell them that you would like it to be that way. Explain to them that you cannot make use of many of the offerings and that therefore they are of no use to you.
Regarding collection management: If you make use of the send to kindle feature you can use your phone or the Kindle management pages at Amazon to sort your books. If you use AZW3 format and copy over via USB, it is more work, agreed.
Regarding Kobo: I have one but I think the Kindle beats it hands down in terms of stability and performance. So if you are easily annoyed by software quirks, your Kindle is already your best choice. (And it has the most reliable PDF support of all ereaders, strange but true).
Plus, Kobo is currently "testing" more prominent "recommend books" ads in their firmware, the kind that you cannot disable or get rid of. So think about that too...
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