Here are a few that rub me the wrong way in my first day of using the Kindle Fire:
It's laggy. The Fire's OS (which is built on Android 2.3) is laggy at times and occasionally you need to touch something twice to get it to respond. It's hardly an epidemic or anything, but it happens more than I'd like it to.
It's jaggy. The Fire's craptastic screen is nowhere near the quality of the IPS panel in the iPad -- and it shows. While serviceable, Fire's rendering quality is poorer than the iPad. Ironically, where this hurts Amazon most is on text. I can see a hint of shadowing around text in books and magazines, and the same goes with Web pages.
Pinch and zoom suck. What bothers me most is the Fire's dodgy pinch and zoom performance. It's both laggy and jaggy. iOS has silky smooth zooming, but the Fire, not so much. Pinching on Web pages is often stuttery and slow the first time on a given page. Zooming performance improves on subsequent attempts (presumable after the page is cached) but it's still not as slick as the iPad. (I'm still not used to Fire's wacky double-tap behavior either, but I'll chalk that up to inexperience).
It's thick and heavy. I guess that I was secretly hoping that the color Kindle would be thin and svelte like the black and white Kindle, but it's not. In fact it's downright horsey. At 0.9 pounds and 0.45-inches thick the Fire feels heavy in the hand. Really heavy. For an extra 0.4 pounds you get the additional screen real-estate of an iPad 2 and it's thinner, at only 0.34-inches thick.
No home button. The Fire doesn't have a hardware home button like the iPad does and it's a mistake. This means that there's no rip cord that you can easily pull to get you home quickly. Because Kindle's home button is on-screen, you usually first have to touch the screen once to see it, then touch the home button. Twice as many touches to do the same thing. I hope that Apple doesn't remove the home button as has been rumored.
It's too small. This one is subjective and some people will like the Fire's smaller, 7-inch form factor, but for me it's too much of a compromise. Maybe it's because I'm used to the iPad, but the using the Fire makes me want something bigger. The Fire's 1024 x 600, 7-inch display is passable for book reading (if you can past the rubbish screen and zooming issues, that is) but 7-inches is a tad too small for reading magazines and Web pages in their full glory. One man's opinion.
No Android Market. Since Amazon forked Android for the Fire, you don't get the Android Market and its selection of 360,000+ apps. Instead you get the Amazon App Store's feeble selection of 10,000 apps. The iOS App Store has 500,000+ apps by comparison. (Update: there's a now a hack to enable Market, but who wants to root their Fire?)
No native Google apps. Since the Fire is running a forked version of Android, it doesn't get access to Google's flagship native apps like Gmail, Google Maps, Google Music, the list goes on.
Limited hardware. The Fire doesn't include Bluetooth, 3G, GPS, a microphone, physical volume controls or a home button (as mentioned above) -- they were ritualitically sacrificed at the alter of Amazon's $200 price point. It's simple actually, don't expect all the niceties of an iPad in a $200 device and you won't be disappointed.
While the Kindle Fire costs less than half the price of the cheapest iPad ($200 versus $500), it's just not worth it for me. I get way more bang for my buck with an iPad. However, if you're looking for an entry-level, lowest common denominator tablet or something for a novice user, the Fire might fit the bill. But a technical user -- or anyone that's used an iPad for more than 24 hours -- will find the Fire lacking in almost every way.