Nelson Shin, you cheap little...
AKOM is a South Korean animation studio owned and founded by Nelson Shin. AKOM is known for its very error prone... ahem... "cost-efficient" animation and is used frequently for American cartoons. Some shows AKOM has worked on include The Simpsons, X-Men, The Tick, Savage Dragon and Batman: The Animated Series; the company was actually fired from the latter because of their consistently sub-par work.
Since Shin also happened to be the producer of the original Transformers cartoon, Sunbow would start using AKOM beginning with season 2. It's somewhat unclear precisely which episodes were animated by AKOM, although it's confirmed that Toei animated 39 of the 49 season 2 episodes[1], which leaves ten more episodes that were shared between AKOM and an unnamed studio from the Philippines[2]. However, as the three episodes "The Core", "The Autobot Run", and "City of Steel" (which all share the same animation/drawing style, hence suggesting that they were all done by the same studio) are widely considered to be of the same quality and style as AKOM's season 3 work, it's highly probable that they were done by them, leaving the remaining seven episodes for the mysterious Filipino studio.
AKOM's participation would definitely increase dramatically by season 3, where they produced literally half the season (Toei only did 13 episodes, and "Call of the Primitives" is widely believed to have been done by Tokyo Movie Shinsha). The short-lived Season 4 (the three-part "The Rebirth" series finale) was then handled entirely by AKOM, as well as all of the season 3 and season 4 commercial bumpers.