I think this is one of the better Transformers series out there. It's on par with Beast Wars in my mind and also a step ahead of G1 itself. Each episode (at least in the second season) had a "to be continued" sense to it, that you must watch the next one.
As for storyline, some criticise it for having a lot of emphasis on organics, something not originally thought to be associated with Cybertron. Though it's different, it's not impossible either. Some may think the Transformers homeworld being half organic is just wrong or unthinkable, but in a previous Transformers continuity seen overseas, Cybertron was destroyed. Had that been aired for all the world to see, you might think differently on the matter. As it were, Cybertron evolves into different states, another golden age wouldn't be improbable either.
Few ever consider that also, Bob Skir, had the first Transformers series here, that had been preceeded by 2 previous TF series that tie into this one. It's often looked past, that he had to put aside some of his ideas to acknowledge aspects from another series. I mean, the original Transformers series set some of the ground rules, Beast Wars followed up, did extremely well following those and coming up with some of it's own, Beast Machines, in it's limited run, had to follow up on those, and didn't have the same amount of time to do nearly so much.
Overall, this was a fine series. I just hope someday, the door will open again to this Transformers continuity so that we may have another follow-up.