I don’t think it’s possible to simplify it to three, mainly because musically the scene is way too all over the place…
you can roughly sum the base of it all to X JAPAN, D’ERLANGER, DEAD END, BUCK-TICK, KUROYUME and LUNA SEA.
but just for the sake of the question, I’d say X, B-T and LS, as they probably covers the most ground possible, influence-wise
it is simply fucked up to leave morrie out, as he is the inspiration of EVERYONE, but oh well…
For me, overall, it’s L’Arc-en-Ciel, GLAY and Kuroyume. I think those three had the best balance of success, longevity and influence on the J-rock/VK scene. But I’m partial to the more pop side of VK, so there’s some of my own bias in there.
I think DIR EN GREY, MUCC and the GazettE would be good picks if we’re talking specifically about the overseas VK fandom, but I’d probably swap L’Arc in for MUCC since I think they’ve got a bit broader of a following because of their anime themes.
This user on note created a list of the bands from that vk genealogy television program I watched several years ago, and it seemed to check out for me (goes up to the 2010s.) You would just have to pick your three from each era:
Subgenres, expanded '85-'99 history, and a top albums list?
ヴィジュアル系のサブジャンルを本気でまとめてみた｜元カノの子供をテリヤキにして食べたい
https://90s-visual-kei-vk.themedia.jp/posts/13152652?categoryIds=1128061
ファン500人が選んだ「後世に伝えたい90年代ヴィジュアル系伝説の名盤」ベスト50 | GALLERY OF VISUAL SHOCK
NUMBER GIRL, Eastern Youth, and Bloodthirsty Butchers
…oh wait, wrong forum!
DIMLIM, 8P-SB, Initial’L,
Maria, Kiwamu, Kisaki
This is dentist’s dreamy top-3
the real vk tree: https://x.com/vr_noru/status/1934884405077836284
Because of how well known and old some bands are, i think they are Malice Mizer (but could be replaced with Buck-Tick), Luna Sea(but if there are any other bands that are considered big 3, you can replace it with them), and X Japan, which is for obvious reasons
I understand many want to include Buck Tick and while I know everything that happened, they haven’t really had that big of a commercial success if you compare to X Japan, L’arc, glay … etc. These bands were also on regular tv shows in japan all the time at the time, that is huge. but i guess we all can define it different and dont care about sales.
Then after all DeG, Gazette and Mucc are the kings for me.
Buck-Tick solos all of them on quality alone, so it all depends on what criteria you want to go with. Commercial success? Maybe not, but influence, quality, and longevity? Absolutely.
generally and in an objective way X Japan, Luna Sea, L’aruku ? the obvious Big 3 !
When I joined the VK craze it was more like GazettE, An cafe, DeG.. but I feel like the first lineup is more “ timeless “ in a certain way
( but this second lineup had the best balance ! cool boys, scary boys, cute fluffy boys, pretty much different styles for everyones taste 
)
truuue, people who says that are mostly Gen Z ! I noticed that this new Vk fans gen are very into Malice Mizer and Buck Tick 
( which is great, because BT were super underrated ( when it comes to general opinion ) back in the days )
I fight so badly back against naming my three which are so painfully biased with no base in reality that this whole thread would implode.
I’m against putting Buck-Tick in a vk-big three because they transcend visual kei. They are doing big packed budokan concerts every new year for a while. They are popular, but not visual kei popular and not X Japan popular. It’s more like wine mom kei kinda vibes
I’d say for j-rock/metal: Loudness, Anthem, Dead End
For vk: the standard Luna Sea, Buck-Tick, X-Japan.
My personal big three for vk: Kagrra, Deshabillz, Syndrome
You can’t just post that without delivering. Come on give us something to discuss 
Dimlim, Nocturnal bloodlust if we ignore the chaotic later parts of their career and R-Shitei
otherwise I would go with
Avelcain, R-shitei and Mamireta
But…okay, you can argue how big these bands are, but they are certainly not old 
Now I know what you meant with this 
An Cafe, SuG, LM.C
X, Aion, and Color hands down.