Very subjective, shaky and conceptual suppositions incoming:
I think that part--just a part--of the reason that there was general dislike for Genthru stems from the fact that, for the longest time, he represented HUNTERxHUNTER’s final boss.
I’m not sure if I remember accurately, but it seemed to me--back in 2005, or so--that you were more liable to encounter someone who’d been watching the anime rather than reading the manga, and with the manga being so inaccessible at the time due to Togashi’s weakness in his artwork, I didn’t get the impression that a lot of people were altogether eager to check out the comic to see if it did venture further than the cartoon.* In any case, when Greed Island: Final finished, it looked as though the series had been done and dusted; despite several story elements still dangling about, it looked like Gon had reached his father in the end, and the final battle to get to that point had been with Genthru--a character who, in the grand scheme of things, represents perhaps but a learning experience in the broader context of the series as a whole. As far as I’m concerned, HUNTERxHUNTER still hadn’t really got off the ground by the time Genthru’s fight rolled around, so when the anime seemed to end with several plot elements still gestating, he came to symbolise the inadequate termination of the intrigue. I like Genthru as a villain, but when juxtaposed against the changeable Hisoka or the esoteric Chrollo--the latter of whom we have witnessed hitherto only but a thumbnail of his history and character--he lacked the resonance necessary for a final boss; and the stage of Greed Island itself and the characters who assumed centre-stage there--Tzesguerra, Goreinu, etc.--cannot function collectively as a denouement. In representing the final boss of the series--and in being a symbol for Greed Island as a finale--Genthru could have been resented for being an inadequate conclusion to the series. After all, Genthru and the saga he inhabits, I suppose, were engineered maybe just as training for Gon and Killua; they’re there as a means to adumbrate the grander and more complex life-and-death Nen struggles that await. Perhaps they're there to illustrate the conflict between the childish video-game-esque world of a child and the malignancy that the adult world, depicted through the literal invasion of the former by the latter--but if this is the case, then Greed Island does not in itself depict the necessary outcome or corollary of that idea: it's the Chimera Ant escapade that does this. Greed Island encapsulates development more than conclusion, I think--though it does something for the former--and in seemingly being shoe-horned into the role as the latter in G.I.:F, Greed Island itself feels as uneasy a conclusion as Genthru, whose presence becomes its symbol, in a sense.
In short, I would suggest that part of the reason Genthru could be resented is that he could have seemed to have been used for a purpose for which he was not intended. Genthru’s significance in the grander scope of HUNTERxHUNTER’s story might not yet even be clear, but the scope that recent chapters--and, more crucially, those York New chapters dealing with the Phantom Troupe and their intentions--have suggested, he could not perforce play the role of final boss. I think that Togashi’s slow rate of publication exacerbates matters in that Greed Island, for me, is not as far a milestone in HUNTERxHUNTER as its placement initially seemed to suggest--and the slow publication rate afforded Genthru a greater presence than he might today have if the series had continued uninterrupted. Genthru can be construed as superficial, and that could hurt the series if it didn’t promise to be as vast as it does. Weaker villains, I believe, can survive in a large series as constructs because bigger and more impending threats are always on the horizon; the side quest for the exorcist on Greed Island illustrates this. For what it's worth, though, I do want to see Genthru come back--because the infrastructure is there to give him greater resonance; and I think bringing him back would bolster the cohesiveness of the story.
* (If they did, I reckon some were deterred by the artwork and were prepared to wait for a new OVA, which meant that they were stuck indefinitely with Greed Island: Final as a conclusion; and the long hiatus around the 2005-2007 period meant that Genthru pretty much was the biggest battle in memory for a long time anyway, in a series that promises much more. Something that was potentially just a formative battle was the abiding memory you were liable to have at the time...which wasn't the nicest thing to go away with.)
Edit: And I suppose that he, as Greed Island's figurehead, represents the series at its most visually challenged--both in the manga and the anime. The former's characters look clunky and incongruous with the elaborate volume backgrounds, and the latter is--in G.I.:F, at least--at its most unenthusiastic.
You're my new best friend. Of course, I'm not saying that Chrollo isn't interesting. He is. But I think he's relatively meh compared to others.
