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.
For the anime:
Broken Base: Either Baku Tech! Bakugan is the best reboot of the franchise, or the worst one ever done by Sega.
Zenoheld's plan started out as enslaving a race for entertainment, then moved on to genocide, and finally to becoming an Omnicidal Maniac trying to destroy the entire universe. He ends up indirectly sending four members of the Vexus to oblivion, and he treats his son like a soldier who doesn't amount to anything else. His own ultimate weapon explodes with him still onboard, his son deciding to go with him to make sure the madman goes down with his ship.
Emperor Barodius is a power-obsessed tyrant who declared war on and earnest to wipe out a peaceful planet to gain more power than he already had. After his defeat by the heroes and imprisonment in an alternate universe for eternity by Code Eve for genocide, He took the alias Mag Mel and began using a Psychic Link he formed with Dan and Drago to leech of their energy to free himslef and Mind Rape them with terrible visions of the destruction he intends to cause on Earth. He's also a firm believer in You Have Failed Me and You Have Outlived Your Usefulness as his disposal of his Co-Dragons Mistress Sellon,even though she'd completed her assignment perfectly and hadn't failed him, and Anubius, robbing him the honor of dying in battle with Dan, proves. If he doesn't kill you for either of those things he brainwashes you into his loyal puppet, as shown when he kidnapped a large number of kids from Bakugan Interspace to brainwash into his loyal soldiers.
Ending Fatigue: The New Vestroia arc. Okay, so the brawlers had to free the Bakugan from the Vexos. Oh wait! Now they have to stop the Vexos from destroying all the Bakugan! Oh wait! Now they have to stop the Vexos from destroying the whole universe!
Mira: First you wanted to enslave the Bakugan, then you wanted to destroy the Bakugan and now you want to destroy the universe.
Ensemble Darkhorse: The Vexos will more than likely never appear again, but after entering the second season after New Vestroia, some of the members are still getting plenty of fan art. And Spectra's popularity was a contributing factor to his return in the latest arc.
Foe Yay: Often overlaps with Ho Yay as well, And IT'S OFTEN! But...the Face Palm-ing Head Desk example is last battle between Dan and Masquerade in Battle Brawlers. The battle was goddamn epic and...well, Intense, complete with collateral damage and...Clothing Damage, well, Masquerade turns to be AliceGehabich. In universe this ain't a problem, out universe? NOT SO MUCH. And the guy in a girl's body tore off his tattered longcoat mid-battle, which exposed bare, feminine shoulders. And the reason he had a breastplate on? To hide a pair of boobs underneath.
Magnificent Bastard: Mag Mel. He's been one step ahead of everyone the entire season. Even when he loses he ultimately comes out on top. Part of this is being an extremely good Chess Master, the other part is manipulating people to play into his hand. Though he's an Omnicidal Maniac, he normally has multiple plans going at once to the same goal so if one fails, he's got several backups ready. While he himself lacks charisma to some degree, he realized this and created two extremely charismatic Co-Dragons to do this for him, to wonderful effect.
Memetic Mutation: VILANTOR! Clearly the most powerful thing on the show, with a currently perfect fighting record.
Mag Mel performing Mind Rape on Dan and Dragon For the Evulz. If not that, then paralyzing a boy in fear to place the Brawlers in a Sadistic Choice where they either have to kill an innocent human being or let Mag Mel's monsters continue to destroy everything in their path.
Coredegon and his gang cross this by being completely willing to obliterate hundreds of humans and Bakugan with absolutely no remorse.
Gundalian Invaders will probably have a lot of Dan/Julie and maybe even some Dan/Fabia undertones
Gundalian Invaders also had some Shun/Fabia, as in the deleted scene of episode 4 where it shows Shun and Fabia talking about the war in Shun's house...at night. It's implied she stay in his house for the night, as she's still shown there in episode 6. Then all the teamwork between them, especially one of the last scenes of episode 34.
Soundtrack Fatigue: The show repeatedly abuses a very slim number of soundtracks from start to finish throughout the entire run, playing them over and over to the point they lose their likeability and border on Soundtrack Dissonance. Normally, this is common with a lot of Long Runner anime, but it's taken to new heights with Bakugan. Granted, there are a few that aren't overused or unique to one season, but when the music tracks start playing in one easily predictable sequence in four episodes straight and you don't get any new ones to listen to that will alleviate the stale music, it gets old fast.
Win Back the Crowd: Mechtanium Surge, thanks to it's Continuity Porn (one of the biggest complaints from fans about New Vestroia and Gundalian Invaders is that everyone except Dan, Marucho and Shun is Put on a Bus) and the surprisingly dark storyline.
Game Breaker: The "H-Bomb". The card "Haos 2" (where you steal one of your opponents won gate cards by having a lower printed power) makes the "H", a "Lowest Power Wins" gate card is the fuse, and a low-power Haos bakugan is the bomb. You win two points in a single round. This is getting increasingly broken as the G-power cap rises and will probably never go out of fashion. The only limit is that you can have only one of each card in your deck.
Game Breaker: Darkus Leonidus with a specific set of 4 cards (one Gate Card, 3 Ability Cards) can easily break 1000 G-Power before adding pickups and whatever is generated in the battle itself. To say nothing about Omega Leonidas with Darkus Attribute and the same setup (substituting one ability card).