2012 was a roller coaster of a year for Apple and those who depend on its ecosystem. It was the first full year Apple operated under CEO Tim Cook's thumb, and there were plenty of ups and downs for Cook to ride on.

We thought we'd highlight five of the most notable Apple-related stories as we look back on the last 12 months. Some directly affect Apple's user base more than others, but they all contributed to a company going through developmental change—on the inside and out. In chronological order…

The removal of Java from OS X Web browsers

Apple's decision to kick Java to the curb was largely sparked by the new (and improved) Flashback malware outbreak earlier in the year. Although Flashback first made an appearance in 2011, the 2012 version took advantage of a Java vulnerability Apple left unpatched for months after Oracle released a fix. That decision to hold off on a fix wasn't the best PR move for Apple, but the company later made up for it—at least in the eyes of security experts—by getting rid of Java in OS X browsers altogether.

"I think that the way they've handled Java in the browser was their biggest win in 2012," noted Apple "hacker" Charlie Miller told Ars recently. Miller pointed out the payoff in writing Mac-specific exploits is still too low for most attackers, but Java exploits carry the benefit of being able to affect multiple platforms at once. "[A]nything Apple does to reduce Java's install base in OS X is a security gain that still gives them some real life improvements."

Tim Cook's public apology for iOS 6 Maps

It's not often Apple issues any kind of public apology for… well, anything. So when it does happen, it means some serious ish is going down in Cupertino. That was apparently the case just weeks after Apple's release of iOS 6. Much to Apple-watchers' surprise, the company posted an open letter in late September to its customers, signed by Tim Cook, that acknowledged Apple's shortcomings when it came to releasing a new, Google-free version of Maps for iOS.

"At Apple, we strive to make world-class products that deliver the best experience possible to our customers," Cook wrote. "With the launch of our new Maps last week, we fell short on this commitment. We are extremely sorry for the frustration this has caused our customers and we are doing everything we can to make Maps better."

Since then, Apple continues to take a beating for some of the weaknesses of Maps. But according to our recent poll, almost a third of Ars readers continue to use the app over other mapping solutions on the iPhone.

The launch of the iPad mini

Some Apple-watchers thought the day would never come, but Apple launched its own smaller version of the iPad only two years after Apple cofounder Steve Jobs declared 7" tablets to be "dead in the water." Apple argued that the 7.85" iPad was different from the rest of the 7" tablet market, not just because of the OS it's running, but also because of its 50-67 percent larger usable area.

Unsurprisingly, Apple declared the iPad mini's launch weekend a wild success, with sales of it plus the fourth-generation iPad setting a new first-weekend iPad sales record. Indeed, the iPad mini seems to be popular enough among the masses—especially as we head into the holidays—at its cheaper $329 price point, even though many reviewers (ourselves included) cried over the lack of a "retina" class display.

Scott Forstall ushered out of Apple

Apple's iOS software head Scott Forstall has always been a controversial guy. He's notorious for being a hard worker with high standards, and he might not always be the easiest to get along with. The latter appears to be why Forstall found himself being ushered out of the higher ranks at Apple in October of 2012. A number of reports cited clashes with other Apple executives as the main reason Forstall couldn't be kept around for much longer. Not only was Forstall allegedly at odds with Apple designer Jony Ive, he also had reported conflicts with engineering head Bob Mansfield, among others.

A little more than a month later, Cook once again hinted at this as the reason for Forstall's exit in an interview with Bloomberg BusinessWeek. When asked about "what was wrong" with Forstall at Apple, Cook was pragmatic: "The key in the change that you’re referencing is my deep belief that collaboration is essential for innovation."

Despite the apparent "jubilation" following Forstall's departure, the news still came as a shock to many of us who follow the company closely. Forstall's influence on the design and direction of iOS is nothing to sneeze at. Although he's staying on as an advisor to Apple, the operating system may soon take a different turn now that he's no longer in charge.

Decision to manufacture (some) Macs in the US of A

There are some jobs that have just plain never been in the US to begin with, and the kind of large-scale electronics manufacturing that Apple does through its Asian partners are some of those jobs. That hasn't stopped the masses from calling on Apple to do at least some of its manufacturing in its home country, largely due to some of the discoveries made at Foxconn's factories in China. In the past, the company has found some evidence of child workers, "involuntary labor," and safety issues, not to mention a recent rash of suicides and disputes over pay in China.

That's why it was both a relief and a surprise when Cook announced this month that Apple would begin manufacturing a line of Macs in the US beginning in 2013. He discussed the decision in his aforementioned interview with Bloomberg, as well as a TV interview with NBC News. Cook revealed Apple has been "working on" increasing its US manufacturing for some time.

"We’re really proud of it. We could have quickly maybe done just assembly, but it’s broader because we wanted to do something more substantial," Cook told Bloomberg. "So we’ll literally invest over $100 million. This doesn't mean that Apple will do it ourselves, but we’ll be working with people, and we’ll be investing our money."

Of course, one line of Macs isn't much, especially when compared against the kind of sales numbers that come from the iPhone and iPad. But the move is symbolic and could lead to increased numbers of electronics—not just from Apple—being made in the US in the future.

Have another Apple story you think should make the cut? Let us know in the comments below.