I've seen that article too and for the most part, their key points are true. But I think the overall main theme of the article (the Free App Of The Day issue) is debatable. Although Amazon's wording was confusing, the fact remains that they knew what they were getting into before agreeing to it.
Amazon hasn't asked to make my app a FAOTD, but the article does help hammer home the idea that not all apps will benefit from it. In particular any kind of app that doesn't have another form of revenue, whether it be ads or a subscription type model. If they were to ask me to consider it, I would likely decline. As far as I know, they cannot force you to do the FAOTD.
Things I agree on or don't like myself:
1) It does sometimes take a while for your app to be approved. I've had updates approved in as little as a few days to about 2 weeks. One thing that is nice though: They do test the apps pretty well and in fact notified me yesterday of an error in my app that I missed and may not have noticed for a while. This error would be most likely to happen to someone running my app for the first time and only under special circumstances but to me it is a big one and could cost a sale.
2) Amazon does reserve the right to change the price of your app. Only a week after first releasing my app on Amazon I got an email stating that they were running a campaign on my app (read: sale). My normal price is $2.98 and they put it on sale for 99 cents. I had no say in it and could not refuse it, and they gave me less than 24 hour notice that they were doing this. While I initially wasn't too happy about it, it did turn out to be my best month at Amazon in terms of profit. Subsequent months have not been nearly as profitable but I still can't help but wonder how much I could have made had they not put it on sale so quickly and practically gave it away right when it first appeared. But then, Amazon knows way more about marketing than I do and it did get my app in the top 10 (+/-) downloads list for a while. On the plus side, other than the sale, they have never changed my app's price.
3) They do rewrite your description. This one really bugs the crap out of me. I don't think they did any better of a job at describing my app than my original description and in fact they kind of left out details that were important to ensuring the app works correctly as it requires third party hardware. Even worse, they left out just about everything that distinguishes the paid version from the free (lite) version. To offset that, I left a review on my own app for the sole purpose of explaining the differences.
4) Their reporting definitely is not as nice as Google's, but it is a little better than before. My biggest complaint is that with Google, I know exactly how much money I will be getting. With Amazon, unless I want to break out a calculator, I can only estimate it. And it is also true that Amazon takes over a month to get your payout from any given month. Google pays out within a few days of the month's end.
5) I know I agreed to it, but I don't like the fact that they charge developers $100/yr just for the privilege of having your app in their store, where they also take 20% of your profits. As I pointed out to them in an email once: Without the hard-working app developers, they wouldn't have an App Store! But to be fair... hand-testing every app in the store takes time and manpower, so I suspect that is part of what that $100 cost is to cover. If your app is free or only sells 3 copies per year, they probably need to recoup the cost of hand-approving all of your updates.
6) Kindle Fire compatibility problems, and from what I understand these have more to do with their special version of the Android OS not displaying things the same as all other Android devices. What's worse is I was told to buy one in order to test my app. Charging us all $100/yr to be in their app store, they should give all the developers a free Fire!
7) Kind of a personal gripe, but after I complained about their advice for me to buy a Fire they handed me off to a specific person who will 'handle my participation in the Amazon App Store' from now on. This is fine, but they were not kidding. I decided to leave feedback on their new reporting tools using their "Leave feedback!" button (and it was mostly positive feedback with a positive and upbeat tone). A couple days later I got a response from someone reminding me that my participation in the Amazon App Store is handled by XXXX and that my message has been forwarded to him. Kind of insulting and (I think) a bit childish. This was feedback on their website that they were asking for, and had nothing to do with my app or its presence in their store.
8) Although the person assigned to 'my participation in the Amazon App Store' was initially helpful, I haven't heard anything from him in several weeks and my app still hasn't been approved for the Fire. Although after reading another thread here, I had a feeling it wouldn't be given their device displays things incorrectly as mentioned above. Unfortunately I had already submitted an update attempting to fix it. Honestly, for now I have kind of given up on the Fire which is a shame because I would bet that many of the Amazon App Store users own one. I do plan to eventually make it compatible but I am trying to figure out how to do that without buying a Fire. It is the principal of the matter, but I have also seen some so-so or bad reviews on it. While I wouldn't mind having a tablet, the Fire would not be my first choice.
All said and done though, I could pull my app and cancel my dev account with them but for now I have decided not to. While the money I make from Amazon is considerably less than what I get from Google, it is extra money none the less. And while the $100/yr thing sucks, I am presently getting more than that per month from Amazon so I can live with it. I also look at it as a bit of advertisement. I think that it's possible that somebody may see it on Amazon and either buy it from them or just look for it on the Android Market. Also, my app has 3 competing/similar apps that have been around longer on the Android Market, but in the Amazon App Store I have no competition.