Through the '90s I remember the Biollante really wasn't all that popular, especially compared what what Toho was currently turning out. Most people did praise the effects and concepts (and rightly so) but were usually pretty hard on just about everything else. And all these years later, at least in my opinion, that pretty much sums up the movie: great effects and so many wonderful ideas, but it comes up short in just about every other area (casting, plotting, editing, music...) I think what's happened in the past 10 years or so is that more and more younger fans are becoming attracted to the darker atmosphere of the story, and are becoming more forgiving about everything else. Keep in mind this is the same demographic and adores GFW, and doesn't understand why the film is so hated.
I really do love Godzilla vs Biollante, and it's the one Heisei film I go back to the most. But it's definitely no masterpiece, and if I was asked to pick a Godzilla film to throw on, a Showa film would win every time. And in terms of the best films in the series, Biollante doesn't come close to Godzilla, Mothra vs Godzilla and Ghidrah. All three of them feel like literally every element of the production came together almost perfectly (I say "almost" because elements of Ghidrah are admittedly rough around the edges), while Godzilla vs Biollante doesn't at all feel like a well thought out film, despite it's strengths.
I've used this example before, but one example of the movie's schizophrenic editing (a result of it's ridiculously rushed production) comes right before the Lake Ashinoko battle. We get a military mobilization sequence that doesn't end as much as the music suddenly stops and a sloppy, fizzy wipe takes us to a shot of Biollante, with Godzilla already at the lake, hiss sudden appearance explained by the fact that an interested entrance scene was filmed and deleted. As Ed explains, it's very clear that the special effects teams and live action teams had no idea what each other was doing, because scenes between the units begin and end without any real cohesion. Then throw in the out-of-place soundtrack and you have a movie that my wife (who adored just about all the Showa films) watched and wasn't all that impressed with.