When I first saw Energon on TV, I thought it was pretty bad. I found a lot of the main characters to be annoying, poor voice acting, you name it.
Then I was convinced by someone to watch the original Japanese version with subtitles.
Wow! What a difference! Characters who are annoying in Energon are actually very well fleshed out and much more tolerable. The two characters in Energon who I liked least (Ironhide and Kicker), became my two favorites (although Ironhide is called Roadbuster) in Superlink! This makes all the difference, as these two are core members of the cast, and probably the closest things to being main characters.
I also really enjoyed the portrayals of Alpha-Q and Megazarak (Scorponok in Energon). David Kaye is always a treat when he does English voices for Megatron, but I found the Japanese voice actor to be very good as well.
It's a very high-energy show with plenty of action, and a surprising amount of character development.
Also, I hear that the Japanese version has a better quality CGI animation. The version sent to the US for dubbing was about not quite complete, as it had to be sent well ahead of time to get the dubbing process started. The Japanese had plenty of time to clean up the animation and still beat the English dub to TV. I stopped watching Energon, so I can't quite confirm, but I've read this on many sources. I also found no reason to complain about the animation in Superlink, while one of the biggest complaints about Energon was in the animation.
I highly recommend tracking down the Japanese version, if you can tolerate subtitles. It's certainly a different animal than Beast Wars, but I found myself enjoying it just as much in the end.