For all intents and purposes, the premise to ALO and GGO is the same - something happens in the game world and Kirito runs off to do something about it. There is also a female player of some description who has her own lengthy plot thread about something or another. Despite this core similarity, I greatly like the GGO arc and greatly dislike the ALO arc. And no, it's not because of the nature of the GGO's thread...well, not completely anyways.
The problem is that in ALO, Kirito's story interacts with Sugu's story (2 year wait, meeting Asuna, etc), but Sugu's story has little to no interaction with Kirito's story throughout the middle of ALO. Yes, there's the whole comforting Kazuto part at the beginning and near the end there are the big reveal and <preemptive spoiler redacting> but the middle chunk really is just a greatly elongated chunk of Lyfa falling in love with the OP stranger. This isn't to say that nothing relevant to Sugu's story happens in the middle, but from my perspective, nothing done *by* Sugu's story interacts with Kirito's.
In GGO though, it's a case of two plot threads that begin as unrelated, collide due to plot devices, actively interact with each other and then resolve together. Emphasis on the
with each other part. It isn't just Kirito's actions that have an effect on the other plot thread - the other plot thread also provides interactions *throughout* the story that resolve Kirito's thread. Another point I'd like to bring up is that GGO's female protag is, in my opinion, worth more than a plot device to Kirito's thread. The constant interactions also come in the form of human to human communication instead of just plot pointers - or running back to my own words, you can't just replace the female protag's story with a bunch of coincidences and still leave Kirito's plot intact.
The second reason I dislike Sugu's story is that throughout the middle of the respective plots, the writing ends up causing both plot threads to distract from each other instead of being complements. Going back to GGO, whenever there is a jump between plot threads, it feels as though the developments are ones that either directly affect or else help bring definition to the other thread. ALO just feels like we're hopping between brains because we can. I even dislike the Asuna-only parts for this reason, despite me considering the Save Asuna thread to be the primary one. Sure it's nice to know that the reason why Asuna and 199 others went missing because of Sugou's science project, but that knowledge doesn't tell me anything about why Kirito or Lyfa/Sugu are doing what they're doing. I'm not sure it had to take an entire chapter just to prove that point and spend an extended period of time trying to emphasize how horrible Sugou is - it could have been much shorter and still served its purpose.
And speaking of justifications, I also feel that far too much of ALO is spent either pulling plot devices out of seemingly thin air, or spending huge chunks of time trying to justify pulling plot devices out of thin air. I can't elaborate further though because then I'm walking on tons of ALO spoilers.