There is so many, because the classification has evolved with time.
At first they just made random elemental strong creatures for example, but by now they set some standards and distinctions, each with different purposes.
So first you have to distinguish between what I call true legendaries, and average legendaries.
=True legendaries are the giant ancient monsters that look like they lived since forever, and are the cause of serious age old stories and local creation myths. In other words, they are a big deal.
-Lugia/Ho-oh
-Groudon/Kyogre
-Rayquaza
-Dialga/Palkia/Giratina
-Arceus
-Reshiram/Zekrom
-Kyurem
By average legendaries I mean all those that we could as well refer to as just super rare powerful mysterious pokemon, with most of them not even having a noteworthy role, except for a nice tale or quest occasionally. Like, they're not legendary, just obviously more special than the rest.
But lets break these down a bit further.
=Semi-legendaries (because they seem related to the true legends in some way and represent the core elementally oriented groups concept):
-Articuno/Zapdos/Moltres
-Raikou/Entei/Suicune
-Regice/Regirock/Registeel
-Regigigas
-Uxie/Mesprit/Azelf
-Cobalion/Terrakion/Virizion
-Keldeo (if it didnt have a deep relation with the musketeers it'd be in the group below)
=Extra/Hidden (they're event pokes, standalone, sometimes gimmicky, just there to add something exotic):
-Mewtwo/Mew
-Celebi/Jirachi/Shaymin/Manaphy/Phione/Victini
-Latias/Latios
-Deoxys
-Heatran
-Cresselia/Darkrai
-Tornadus/Thundurus/Landorus
-Meloetta
-Genesect
----- I II III IV V
True 0 2 3 4 3
Semi 3 3 3 4 4
Extra 2 1 4 6 6
So as you can see, the True legends only appeared gen II on, but along with the Semi legends, they both stay quite steady throughout the generations.
The only thing that actually changed is the number of Extra legends went uphill for some reason.
And I believe those are the ones that concern most people.
You know, stuff like LAti@s, Heatran, Meloetta..
They all seem kind of random and uneccessary.
Therefore I can see why people might be upset about it, but personally, none of those are bad enough for me to agree, since they always have some interesting seperate thing going on, ie the lunar duo with their mirrored islands, Meloetta being dedicated to music and so on.