The core three Go-Busters in general, as many feel they lack the character development needed to be truly interesting characters. Hiromu didn't move on from his parents' death. Yoko and Ryuji seem to enjoy their life without their parents too much.
Broken Base: Over whether or not the season should have been skipped by Power Rangers for Kyoryuger.
Enter has proven to be quite popular amongst fans, who like him not only because of his enjoyment of being the bad guy, but also due to being a quite credible threat, being able to go toe-to-toe with the Go-Busters in fights and succeeding in several of his missions. His proving to be very clever and learning for his mistakes as the show moves on has made fans like him even more.
Among the heroes, the most popular character is, oddly, Usada.
Now we have Beet Buster and Stag Buster. Their hilarious antics and awesome design and fighting style really help.
Evil Is Cool: Enter. Whether it be his plans, his calm way of speaking peppered with French, or his character design, everyone seems to agree Enter is one of the best villains in Super Sentai history.
Since the 'exporting' of Super Sentai internationally under the name Power Rangers is old news by now in Japan, the whole premise of Rangers protecting their world's power supply (the whole Enetron shebang) may have been Toei's attempt to create literal Power Rangers.
One old rumor before Go-Busters aired was that Gavan would be the teams mentor. Thirty episodes later, guess who appears? Well...Mind you, not the one we were thinking of.
In #33, the Powered Custom Super Mode involves an addon to the morpher that fuses our heroes bodily with their Buddyroid partners...kinda like CycloneJokerXtreme. As if reinforcing this, Red sticks to close-quarter combat (like CycloneJoker), Blue summons a girder that he uses like a staff (HeatMetal), and Yellow sticks with the shooting (LunaTrigger)!
Ryuji was not the first blue ranger to have problems with overheating. Gosei Blue had in one episode too and, while Ryuji gets psychotic, Hyde gets HILARIOUS.
And in Mission 49, he goes even further, assimilating an Enetron tank, turning it into a Megazord, along with dozens of innocent employees. He even attempted to absorb children! And his final plan has him doing this all over the world. As if we needed any more reason for him to be deleted!
Enter after his defeat in Mission 30. Somehow him becoming more stoic and calm with only occasional traces of his troll-like persona remaining. Somehow this makes him even more disturbing than he already was.
Escape's Megazord's debut. She takes Enter and CRUSHES him using the Megazord's hands. It's pretty graphic for a show like this and there's the crushing sound to make everything better.
The core three busters in general. They become a base breaking characters with enough character development. They went from wanting to save their parents to not letting their sacrifices to be in vain and accept their death. Also, they become noticeably closer than before.
Robo Ship: Usada and Yoko. Later, Yoko and J get paired up often.
Special Effect Failure: when in close-up shots, the Buddyroids' eyes just look like glow-in-the-dark stickers.
Let's not get started with the Go-Busters themselves, who would have gotten Character Development if the staff put more effort on them.
They Wasted a Perfectly Good Plot: Messiah's origin is never revealed. Being a computer virus, one would think that it'd be a man-made entity, and some speculation is made regarding its origins (perhaps the scientists at the facility, or even Hiromu's parents created it). It would have made for an excellent reveal during the late stages of the series, but it was never even hinted at or touched on.
Tough Act to Follow: Quite a few fans think Go-Busters is a great show, but had the misfortune of coming after Gokaiger, which was brimming with awesome. It's worse if you compare it to Kobayashi's previous Sentai, Shinkenger, where the cup runneth over with epic dramatic awesome every single episode.
Uncanny Valley: An intentional case. Hiromu's face on Enter's head is very... off.
Vindicated by History: The season has enjoyed a resurgence in popularity for the same reasons people derided it at first (being too different). Especially from Kamen Rider fans and people disappointed with Kyoryuger, ToQger, and Ninninger.
It's also earned a bit of pity from various fans in both the West and the East after the announcement that Power Rangers would primarily skip it in favour of Kyoryuger.
It doesn't help that the Go-Busters became supporting characters in their own team-up with the Kyoryugers, with part of their time given to the Zyurangers and Abarangers. Fans were similarly upset when this became known.
Notable is the almost complete lack of stock footage, especially when the previous season was full of it.
Wangst: Hiromu. Everytime he's not acting stoicly, being scared by chicken or kicking Vaglass butts, tends to whine, especially over his missing and now dead parents. When Enter reveals that he has the last Messiah Card in his body, Hiromu even considers killing himself in order to kill Enter. Seriously?
Anyone who face the same situation as his will do the same thing.