While there are lots of good reasons to use Draft2Digital, Smashwords, or any of the countless other aggregators available, we would always recommend that you publish directly to Kobo via Kobo Writing Life. The majority of aggregators will allow you to opt out of distributing to specific retailers, so you can choose where to spend the time uploading directly.
One of the most important reasons why authors choose to self-publish is control, and publishing directly allows you to retain all control of your books at Kobo. We cannot remove or make any changes (metadata, prices, etc) to books that were published through another source, eg. Ingram, Smashwords, Draft2Digital, Streetlib, or any traditional publisher, even when the author requests it. The distribution agreement that Kobo has is with the direct publisher/distributor. We're legally obliged to receive the permission of the publishing entity before we make any changes to a book.
By publishing your books directly, you can access your books via your author dashboard, make quick changes and updates without having to go through a third party. You can choose whether or not you want to opt into the Kobo Plus subscription program (you can even choose which territories you want to opt into) and you can decide if you want to distribute to libraries.
Each retailer should be treated individually, as each serves a different reader base and will offer unique opportunities. It's worth getting to know the nuances of the various retailers and learning how to sell to their readers.
For example, Kobo offers unique opportunities for direct authors with regards to promotions. Our unique promotion tool is built directly into the Kobo Writing Life dashboard, and we also offer audiobook and OverDrive promotions to authors who publish directly.
Finally, remember that aggregators take a cut from your earnings for handling your content. At Kobo, authors earn up to 70% of the list price on every book sold. While only you can decide if this cost is worth the convenience of using an aggregator, keep in mind that going direct will allow you to maximise your earnings as an indie author.