For myself I largely could care less about a stores apps, etc. I'll generally buy from whoever is cheapest and/or I might have a coupon or giftcard for. Format isn't a huge concern and my library has books that were initially ePub, various Amazon formats, LIT, PRC, eReader/PDB, etc.
All of my books go into Calibre and if not ePub already get converted. They're transferred to CC on my iPad mini as ePub's for reading in MapleRead, and if I want them on an eInk device are sent to my Aura HD. I prefer kePub on the Kobo, but kePub conversion is setup to be handled automatically during transfer so I just don't worry about it.
For ePub stores my choices (prices being equal) would be 1) Kobo, 1a) Google, 2) eBooks.com, 2a) BAM, 3) B&N, 4) Misc publisher & author websites. I rarely need to look beyond Kobo or Google.
Any of the others stores are largely relegated to someplace to buy either if there is a special deal/coupon/offer or a rare time when Kobo or Google (or Amazon) doesn't have it, which used to occasionally happen, but would be rare this late into the game. If I can't download a copy to put in Calibre (such as pubs who use BookShout) I don't buy.
My only real "con" with Kobo would be if a book can't be downloaded as an ePub and I have to jump through some minor hoops and get a kePub and work from that, but I don't even know if that's an issue with them any more to be honest. Haven't run into it in years. Have also run into a problem once with Google where if an eBook was in the 100's of MB's the ePub wouldn't download only the PDF would (this was some problem in their system according to support), but books of that size are rare and like my Kobo issue it was years ago and may or may not even be a problem any more.
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