This is also true for the current run, Transformers Animated. I think the gasp of displeasure I let out when I first saw the series new, "hyper animated" look is still floating and full audible somewhere in the space surrounding Cybertron, but the more I see of the show, the more I'm coming to realize that despite it's art style, it is an otherwise decent rendition.
The second season show is a direct continuation of the first. Although it does a reasonably good job of catching newcomers up, the general expectation is that if you're watching this season, you're already caught up on the overall plot. The season picks up in the aftermath of the showdown between the newly rebuilt Megatron and the Autobots. Most of Detroit is left in ruins and the Allspark has been shattered and is seemingly lost.
As a result, the Decepticons have retreated to an underground base to lick their wounds and regroup while the Autobots are left with a bit of a PR problem. Although they were hailed as heroes and accepted by the humans in Detroit, they are now seen as a menace. The only person who still sees the robots as heroes is their human ally Sari, but she's currently occupied with trying to find her father, who was kidnapped by Megatron and forced to reverse engineer a Space Bridge so the Decepticons can stage a sneak attack on Cybertron.
To make matters worse for the Autobots, the Cybertron Elite Guard - Ultra Magnus, Sentinel Prime and Jazz - show up on Earth to retrieve the Allspark. They don't take the news of the Decepticons or the Allspark's fate all that well and hold the Autobots responsible. In particular, Sentinel Prime seems to have an axe to grind with Optimus and does everything he can to undermine him. Eventually, it is discovered that the Allspark isn't destroyed, just shattered, setting off what I'm sure will be the series' main driving force for the rest of the run. I'm not sure if I like another "let's collect everything" based plot, but at least the individual episodes manage to center on other things. It will be interesting to see how this develops into the next season, since it could potentially sink the series.
In general, each episode follows the same pacing as the first season. Each is self-contained, but at the same time, the events also play into the larger plot. I think that's one of the major advantages of reboots like this; it allows the show to keep their continuity in place. Transformers Animated: Season Two is particularly good at this, which is to its credit. Admittedly, some of the episodes are weaker than others, but everything eventually fits.
As with the first season, the Autobots face off against both human and robot foes. Several human villains, like Headmaster and Meltdown show up, as do several robot villains like Blackarachnia. Several new characters are also introduced. Season Two finally introduces Megatron's agent on Cybertron, Shockwave, and the Constructicons (though no Devastator) as well as two movie throwback characters, Wreck-Gar and Blur.
The episode featuring Wreck-Gar is easily one of my favorites of the season. Not only does "Weird Al" Yankovic step in for voice duties (a bit of a reference to Wreck-Gar's theme song from the original animated movie), but he finds a way to work in at least two song references. The references to the original Generation One (G1) series don't stop there. The original Spike also pops up in an episode and if I'm not mistaken, he's even voiced by the same actor as the G1 series. Though it shouldn't be taken as a direct link between the two shows, I'm always appreciative of little nods like this to long-time fans.
Compared to Season One, Season Two takes the extras a little further. Audio Commentary is provided for Episodes 19 and 20 and two animated shorts are included. The commentary is sort of interesting, though it didn't hold my attention well. The same goes for the shorts, which were a little too goofy for my tastes.
Although I'm still not completely sold on the series, Transformers Animated: Season Two continues to impress me. As mentioned in previous reviews, the art style is still the series' greatest deterrent, but it fits the series target audience, not a bunch of twenty-somethings with misty childhood memories. Again, younger fans and more open-minded Transformers fans will enjoy the series, but if you're not in either group, skip it.