Wow, I just finished watching Season 3 as well. Overall, I loved it and I think the tight storyline and character interaction is superior to the original US Cartoon.
However, some things I was disappointed with...
[SPOILERS AHEAD for those that have not watched it]
- Rhinox and Inferno seemed underdeveloped for characters that lasted for most of all three seasons
- The end fight between Optimus and Megatron was kinda disappointing, Optimus was made out to be weak and hardly tough enough.
- Certain references, such as Megatron donning a judge's wig in the trial of Quickstrike, and the references to animosity between cats and mice, implies Cybertronian culture has strong similarities to Human culture, something that I do not find credible (but there may be things I am not aware of)
- Plagiarism of Christian eschatological thought in the Covenant of Primus (references to "alpha and omega", and lifting parts of Revelation 12). Not a major problem, but I had hoped for more creativity (i.e. at least come up with your own quotations and prophecies perhaps?)
[END SPOILERS]
I realise when watching / reading fiction, a certain amount of suspension of disbelief is required. So I did my best to overlook those points, and found the show to be quite enjoyable. :)