These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
YMMV: Transformers Cybertron
Good Colors, Evil Colors: Played with at times, Played Straight at others. Quite a few good guys tend to have red auras, while bad guys often have purple. Autobots' weapon fire is always red with red-and-white explosions, while Decepticons' blasters always have blue beams with purple-and-yellow explosions.
Crowning Music of Awesome: Crowning Soundtrack Of Awesome (although some would say more so of Galaxy Force than the US remixes/editing)
Most of it was unchanged, the US Version just didn't use the Japanese vocal songs. It also inserted Our Ally into a few places where it worked better than the original track. Such as Optimus Prime's last clash with Galvatron.
Some fans would say it changed the mood.
It did, at that. To some of us the change is welcome. For instance, the use of Our Ally in that last battle made the mood more heroic than somber. Likewise the use of Fierce Battle! Super Mode for the final leg of Galvatron vs. Starscream made it feel more dramatic. But both can easily be viewed on YouTube, so take your pick.
Vector Prime is one of the show's biggest enduring elements, and arguably the most popular member of the Thirteen (and it's only "arguably" because The Fallen got a movie). His Fourth Wall Mail Slot (and its subsequent Insecticomics parody) certainly didn't hurt.
The Scrappy: The human children that inevitably follow the Cybertronians around are usually the scrappy in their series. This was averted for this show, partly because the kids actually had more interesting personalities, but mostly because they weren't Kicker.
Woolseyism: The dreaded "uh" and "gimme a break!" of Energon is gone, replaced with what constitutes playful romantic banter when both speakers are in their early teens. Homages and an all-new cast turned into known characters a la Transformers: Robots In Disguise, as well.
But mainly, there's the phenomenon that the Transformers Wiki calls "Burning Justice". Galaxy Force was the most "Anime" of the Japan-original Transformers series by far, and the reality-bending powers of wanting something really really hard could make virtually anything happen, with no one treating it as unusual. For Cybertron, this is excised by tying the effects to artifacts that could actually do the things that happened for no reason at all when someone yelled or grunted in the original. It was done so perfectly seamlessly you'd be shocked if you knew the full extent.