My take on the storylines:
Vok plot - This one started out really good, all through Season One. There was mystery, there was intrigue, there were also a lot of cool action scenes and big explosions. The stories were almost poetic in their execution. Season Two rolled around and we got Other Visits Part One and Two. Don't get me wrong because they were really well-animated and well-written but they felt pretty empty. I mean, for one thing, after six episodes of unsolved mysteries dedicated to the Vok(along with two episodes that hint at them remotely), you'd think we would learn more about them. But no.
Instead, what we get is the abduction for Tigatron and Airazor. And for what? So that they can get replaced with Silverbolt and Blackarachnia who later on dig up the Ark and let Megatron prance right into it to destroy time and space? In the end, we learn nothing new about the aliens and we lose two cherished characters for no apparent reason.
Then third season rolls along and we see that the aliens are two giant voodoo glowing skulls. Somehow, I was expecting a little more... maybe like an entire civlization or them or something. I guess it's just like that show
Lost. The revelations and answers to our questions never live up to their hype. Maybe if Beast Wars had lasted another 13 episodes(or more ideally, 26), then maybe the Vok storyline could've been expanded on a lot more. Who knows.
Dinobot's storyline - Dinobot used to be my favorite character at one point. Nowadays, he barely scratches the surface of my top five but I'll still give credit where it's due. The episodes that concentrated on his character were for the most part phenomenal. The guilt and shame he felt over his betrayal of the Maximals were very real. He realized that he had become untrustworthy, not to mention hypocritical. Then he sacrificed himself in the heartfelt episode that many of us consider to be perhaps the greatest Beast Wars episode of all time. His story was brilliant and touching.
Protoform X's tale - My personal favorite. If I could go any deeper into how awesome Rampage is, I'd have to write an essay that spanned many paragraphs. But I digress. Rampage introduced a completely new facet of the Beast Wars. We find out that the Maximal government isn't exactly all full of sunshine and happiness. We also see the traumatized victims of his attacks in the form of Depth Charge. It's a psychological drama's paradise from there on. The way they died was also moving and climactic. My only complaint is that Rampage is in a total of 13 episodes while DC's only in 7. I wish they had lived longer... But anyways, Rampage owns you. Don't ever forget it.
Maximals & Preds find out they're on Earth - Leads up to the Agenda trilogy. Pure brilliance. 'Nuff said.
Protecting the Autobots in the Ark - Most of the Maximals start getting more jaded and cynical. Optimus is no longer as corny or as entertaining as he used to be.
High-strung and jaded Maximals = Meh
Standalones - Most of them from Season 1 are underrated gems. You don't have epic, high-octane story arcs like the one in Season 2 without standalone episodes like the ones from the first season to build up characters so that you can care for them and get a good feel for 'em as well. As much as I like Season 2, a part of me wishes that the first season had gone on indefinitely.