Computer-generated imagery (CGI) in Transformers media has gone through four phases thus far.
The Generation 2 "cartoon" was simply the Generation One cartoon with a new CGI opening, and new scene-transitions featuring the nefarious Cybernet Space Cube. These segments added nothing but glitz to the cartoon, and are mostly forgotten.
The Beast Era
Both Beast Wars and Beast Machines were fully CGI, created by Mainframe Entertainment of Canada. Beast Wars was a bit primitive, even in its day. (It is notorious for lacking shadows except when vital.) Its animation quality improved steadily over time, most obviously in comparisons of the landscape between first and third seasons. Beast Machines was a further step forward, and holds up reasonably well even by modern standards. Both are praised for their good use of facial expressions and body language.
Energon and Cybertron
The last two-thirds of the Unicron Trilogy, Energon and Cybertron, both used shaded CGI for the Transformer characters, and traditional cel animation for almost everything else (humans, backgrounds, etc.). Some episodes (e.g., "City") used CGI for doing complex environments, particularly when the camera needed to be able to move through the city quickly.
In comparison to the Beast Era, the character animation in Energon and Cybertron is generally unimpressive. For an extensive discussion of its flaws, see Energon, Production flaws.
On the positive side, the character models are toy-accurate to a fault, reproducing the design and transformations of the toys in detail.
After 10 years, another fully CGI cartoon show has been released.
- If one includes the Generation 2 cartoon, then of the nine Transformers TV shows that have aired in the U.S., more than half have used CGI, and nearly half have used it extensively.