- The back story and overall impression of the Heisei era is one of its strongest aspects. The elements set up are really fresh and intriguing with lots of story potential. It's impressive how, despite being the successor to the much longer and more varied Showa films, manages to not go over ground all ready covered.
- The music. First of all, Reijiro Koroku created one of the finest scores in the franchise. It's a dark and powerful, but with a sense of campy operatic grandeur that suits Godzilla perfectly. It doesn't get sang enough praise, IMHO. Why he wasn't asked to return for Godzilla vs. Biollante is beyond me and it's a shame that he wasn't. Secondly, Akira Ifukube, when not creating some of his best work, was ironing out classic pieces to be re-used.
- Special effects bits. Era has my favorite Godzilla roar, Mecha King Ghidorah is friggin' cool, Biollante is an incredible creation, and there's some damn-near-perfect work to be had in The Return of Godzilla and Godzilla vs. Biollante in particular. The matte work is flawless overall and easily one of Kawakita's strongest talents. How we got embarrassing scenes like Godzilla coming ashore in Godzilla 2000 I will never know.
- "Adding on" to the Godzilla mythology. Doing what any good "reboot" should do, the Heisei films (starting off and finishing specifically) did a good job of respectfully building onto established mythos. In The Return of Godzilla we learn that Godzilla absorbs radiation; an idea that seems completely obvious in hindsight. Godzilla vs King Ghidorah throws in the novelty of seeing Godzilla "pre-1954" and of the Godzillasaurus (a concept I'm not entirely sold on, but is novel and appropriate enough). Godzilla vs. Destroyah sees Godzilla's own greatest source of power being his downfall. Those sort of things.
- Has a diffident "Beginning, Middle, End" which makes it feel like a saga. It's only natural that this series would end in tragedy and Godzilla's death. Even a creature like Godzilla, living in a world that has dedicated absurd amounts of money to the creation of Superweapons that exist only to kill him (and rightfully so), would die eventually. Why people think they should reopen a Saga that was closed just right is beyond me.
- The Heisei Godzilla is a floppy, chunky mess overall. Despite having interesting design flourishes I'd like to see return (shark teeth, dark eyes, roar, etc.) it's a mediocre design.
- Miki, while useful and interesting in Godzilla vs. Biollante, her status as the defacto human protagonist and her bizarre shift to sympathizing with a Godzilla that is, for all intents and purposes, a skreeonk makes her annoying. She's tragically over-rated.
- The plots are vague and contrived. The entire process for the creation of King Ghidorah is a good example, as is Spacegodzilla.
- All the original monsters, with the exception of Destroyah, are just clones or effectively "repaints" of another monster. Biollante? Godzilla DNA. Mecha King Ghidorah? Cyborg Ghidorah. Battra? Evil Mothra. Spacegodzilla? shitty Godzilla. Lame.
- The effects work after Godzilla vs. King Ghidorah was just sloppy and lacked refinement. A perfect example that pretty much explains every problem with the Heisei effects work (and I think Arrow has pointed this out before) would be in Godzilla vs. Destroyah where Godzilla is matted perfectly into the city scape of Hong Kong...and there's people just sorta' walking around not looking to be in a hurry. That sort of thing peppers the effects work all over the place in these films and there's basically no excuse for it.
“I have never listened to anyone who criticized my taste in space travel, sideshows or gorillas. When this occurs, I pack up my dinosaurs and leave the room.” - Ray Bradbury