That was an intentional short sighted decision made during the second half of the Eisner year. With the acquisition of these brands, Disney, both the company and the BRAND, have been hemmed into a corner, not unlike a multi brand car conglomerate like GM.
Think about it. General Motors was formed over time through the accumulation of successful car brands with the reasoning that a larger organization could help all of them design, manufacture and sell cars whilst focusing on particular verticals. Chevy was the everyman's brand. Pontiac was a sportier version of Chevy. Buick and Oldsmobile are a step up from the everyman brands, but still affordable. Cadillac was the car that the successful man graduated to over a lifetime of car ownership because of its status as the elite American automobile. I've chosen to leave out brands like Packard, Saturn and Hummer, but you get the idea.
What Iger has done with his BRANDed strategy is effectively the same. Bob didn't say, "Disney has been excluding boys from its audience, we ought to expand the tent." He instead bought brands like Pixar, largely general neutral, Marvel, strongly identified with young boys/men/comic book guys, and Star Wars, perceived to be male centric, but more gender neutral than most realize. Today's Disney can remain largely a young girl's brand under this arrangement. Wildly successful non-princess female characters like Doc McStuffins and Judy Hopps are the exception when it comes to what has been pushed under the Disney moniker in this period. Aside from Mickey and friends, the princesses are the first thing that comes to mind when you say Disney. During Walt's lifetime, the company made three "princess" movies, out of 19 features. The Lasseter/Catmull years at Feature Animation alone will yield at least six, roughly half of the studio's output. Disney Junior, except for a certain MD, features largely gender segregated programming. The Disney Channel is defined by its tween sitcoms. For a generation of children, Disney is a girl's brand.
The problem with using BRANDs for market segmentation, as practiced by GM and today's Disney, comes from change, both the ability to adapt to it and to grow beyond what you are traditionally known for to embrace new opportunities. If corporate brass decides "this is what Disney is" or "Marvel is for boy's first', the company severs the opportunity to change. GM's brands faired poorly as the fifties gave way to the sixties, followed by the seventies and eighties and so on. Many of GM's once iconic brands like Packard, Pontiac, and Oldsmobile are long gone because they got left behind, optimized for a bygone era. Rising gas prices and the higher quality foreign imports from Germany, Japan and Korea decimated GM and the Big Three's stranglehold on the American market. GM's response consisted of creating new brands like GEO and Saturn to appeal to the same people who used to buy Chevys, but found Toyotas and Hondas better suited to their needs. Only through decades of painful layoffs, ignoring promising ventures like NUMMI and EV1, a government bailout, bankruptcy and restructuring has GM become move adaptive to change.
Iger's Disney, and its choice selection of BRANDs, are optimized for today. The bets paid off very nicely for the company. However, success hides problems. Like you note, Disney is still painted into the same corner it was in 2005, a BRAND for young children, particularly girls. At present there is no incentive for Disney to expand to the place where it should be, a producer of entertainment for all ages and genders, because the BRANDs it controls effectively cover this, for now.
Eisner's Disney, by necessity and perspective, wanted to build a bigger tent for Disney. Disney needed to change and grow, and it did. At the height of the Eisner years, Disney was as big as it was in Walt's day. Even as things went south in the second half of his tenure, the
need to expand and strengthen Disney under that name, and everything that comes with it as a point of pride and ownership, remained.
Disney hasn't endured for almost 100 years as General Entertainment, nor will it.