Fanbois don't always think rationally ...
I'll preface this post by saying that i'm not an Eisner hater. I mostly agree with your comments about him in general and liked a lot of what he did (though I have some complaints with his reign as well). I'd say i'd easily take him over Iger at this point and would have preferred Eisner had stayed to see what he could do to clean up the mess. What I did want to do in this post is provide some thought on how I think the fanbase came to its conclusions in the first place.
I think a lot of the perceptions of Eisner in the fanbase isn't so much a lack of rational thought (some perhaps but certainly not all), but more a lack of contradictory statements that paint Eisner in a more positive light. The fanbase came to its opinions due to a variety of surrounding circumstances happening to the company at the time, as well as the spin the other corporate leaders were creating against Eisner to the public (Roy Disney Jr also got the fanbase incited against Eisner). Regardless of how much direct blame Eisner deserves for the company's decline during his reign, even the few of us who actually liked a lot of his decisions (or at least don't hate him outright like many do) still concede that he made some pretty damn harmful decisions in his later years. At the very least he allowed things to get too out of hand before it was too late for him to make fixes. Some of these problems the company still hasn't recovered from. But many people do hate him, and I can say that to some extent I do understand where they're coming from. Except for those who think Iger is somehow nearly as good or better...
The fanbase in general really doesn't have much understanding about how the inside of the company works. They have very little to go on- basically from whatever political spin is wrought by the company, and by looking at their surroundings. Now even if you disregard the corporate spin against Eisner, the fanbase still saw his last few years as looking unquestionably dire from an entertainment perspective. Arguably a lot more bad decisions than good ones, some permanently scarring the company forever in ways. The US parks over the course of just a couple of years were morphed into absolute messes, horribly maintained and losing many classic rides/attractions with poor or no substitutes (not to mention making bad and inappropriate thematic alterations). The general opinions about new parks have been pretty meh to negative, with the exception of Disneysea which is adored and considered one of the best out there. California Adventure wasn't very liked at the beginning (it took Cars Land for the fanbase to start giving it serious love). Walt Disney Studios Park in Paris is considered by many to be the worst park Disney has ever built. Hong Kong DL (despite your own feelings or how good it has become in the past few years) was initially considered a disappointment due to the crippling lack of rides. After Treasure Planet there were now several core theatrical Disney animated stink bombs in a row (the plots sucked, and Eisner also made the mistake of killing off traditional animation and burning bridges with Pixar). The direct to video sequels were almost all awful. The Disney Channel (excepting the few successes like Kim Possible) was putting out more garbage than good, such as the teen sitcoms and the made for TV "original movie" crap. One of the few unexpected movie successes during that era was ironically Pirates of the Caribbean. But on the flipside, the Haunted Mansion adaptation released around the same time was terrible.
By the time the Disneyland cleanup happened along with the construction of Everest (the most exciting new WDW attraction since the 90's), Eisner was already in the hot seat with the other leaders and about to be replaced. The fanbase I think sees Eisner's last couple of good decisions more as acts of political desperation to maintain power rather than legitimately caring and trying to fix mistakes (even though that may have been what it really was). Either that or decisions forced upon him rather than his own. So, given the surrounding circumstances along with what information they were being fed (again from people like Roy Disney Jr), I can't blame the fanbase for directing such hate towards Eisner. Some of that blame has to at least indirectly fall to him (even if others were more directly responsible). An outstanding leader (though he was one initially) does not allow a company to spiral out of their control like that.
To this day there really aren't a lot of people like yourself (or even myself) who care to show Eisner in a more positive light, at least Eisner's later years (most people seem to agree the first half of his rule was excellent). And usually when someone praises Eisner now, it's to show how horrible Iger is rather than to show how great Eisner was. I find your comments about Eisner fair to a large extent, but there were legit reasons to hold distaste towards decisions made by the company in the later years of his reign. Even if Eisner is eventually perceived in a more positive light though, he is still going to be perceived by many (and this is fair in some respects) as having poor leadership skills during the last few years of his rule. I don't think he was a poor leader in that he's like a tyrant who is deliberately out to ruin a company and screw the fans in order to make a quick buck (like Iger), leaving the company to burn in his wake. I think Eisner was a leader who had good intentions but let things spiral out of his control. You can make as many excuses as you like that he wasn't at fault for some of the things people blame him for, but as CEO at least some responsibility has to fall to him.
The irrational thought in the fanbase comes from people who hated Eisner but somehow like Iger (thinking he's as good or better as Eisner). I can at least see why someone wouldn't care for Eisner in his later years based on circumstances and such (I myself am far from positive about that time period), but I can't fathom why fans could think Iger any better.