I swear, this won't become a thing for me....I hope.
Anyway, I may be weird, but I have a tendency to group legendary Pokemon (from Articuno to Genesect) in a different category from regular Pokemon. I also group fossil Pokemon separately, but that's another story. With so many legendary Pokemon now, a top 10 list seems quite feasible.
I will freely admit when I'm wearing nostalgia goggles and this is one of those times, so expect a lot of Johto Pokemon. Here we go!
10
Articuno
Articuno is by far my favorite Kanto legendary. I mean, I guess Zapdos and Mewtwo are pretty cool, and Mew is cute and all, but Articuno is just so beautiful. That's right, its gorgeous design is the only reason I love this Pokemon. Let's face it, the legendary birds don't really have a "story" to speak of, and Articuno's combat prowess are...less than stellar, but its graceful and beautiful design has warmed me enough to it that it makes this list.
9
Giratina
Giratina, I didn't care too much for in Diamond and Pearl. I appreciated its unique typing and the fact that we finally got a Ghost type legendary, but it never spoke to me...until Platinum. I think Platinum had the best story of all the games in the Pokemon series so far, and that was due in no small part to how they handled Giratina and the Distortion World. Platinum skyrocketed my love for this Pokemon. A lot.
8
Reshiram
It's a Fire/Dragon (an actual one, not a poser like Charizard) and it looks like a freaking angel dragon beast of holy doom. What more do I need to say? I prefer Reshiram over Zekrom because I'll take graceful and elegant over tough and "badass" any day.
7
Kyogre
Arguably the best Pokemon in the game with its rain boosted STAB Water Spouts and 100% accurate Thunders in the perma-rain which it summons. Kyogre is my second favorite Water type legendary. I like its design and its badassedness, but frankly, I mostly like it out of loyalty for Pokemon Sapphire, my very first third gen game.
6
Ho-Oh
Ho-Oh is actually pretty cool, despite its 4x Rock weakness. I freaking love its backstory in the Johto games, and I especially love the fact that they kept it mysterious. While I do like that the newer games are exploring each legendary's story, I do think there is something to be said about legends that are still...well...legends at the end of the day. That's kind of why I really like Ho-Oh.
5
Raikou
Take Ho-Oh's fantastic myth and backstory, add a lightning saber tooth tiger shaped mythical raiju carrying freaking thunderclouds in its back, and throw in a bit more mystery for good measure (what did it use to be before it was reincarnated?) and you have Raikou. The most badass electric type I have ever seen. Forget Luxray or Manectric, this thing is my all time favorite Electric type Pokemon.
4
Virizion
It's a Grass type, do I really need any more reason? What's that? I do? Darn... Oh well. I guess I like Virizion mostly for, you guessed it, its elegant and graceful design. I actually don't particularly care for its backstory, but it is based on one of the Three Musketeers, so bonus points for that. It doesn't really have much of a personality on its own, but the collective musketeer trio's parallel to the source material which they were based on is actually pretty good. I also like that it's a complete monster in battle.
3
Celebi
Well, besides being the very first Grass type legendary (MAJOR bonus points for that,) Celebi is also a very mysterious time traveling fairy sprite. What does it want? What is it after? How many of them are there, just one at different points in time, or several separate Celebi? Why does it protect Ilex Shrine? I love all of these unanswered questions in Pokemon mythos, which is something we don't see quite as much of today.
2
Suicune
And again, grace and elegance. Plus its a Water type. And its based on the Kirin. And it looks like a wolf. And it has an even more mysterious story than the other two beasts, if Crystal and HGSS are anything to go by (why is Suicune more important to Eusine than the other two?) Also, and I'll freely admit this without shame: nostalgia. Crystal was the second game I ever had that I got my team to level 100. It was the first time I used Meganium, and the first time I trained Tyranitar and Kingdra. Suicune represents all of that, so it gets to my second favorite spot because of it.
1
Lugia
Let's face it, Lugia really has a lot of points stacked in its favor. That badass yet sleek design, the star of the movie Pokemon 2000, the mascot of Pokemon Silver, a signature move in Aeroblast, insane defensive potential on the competitive side. Unfortunately, when it came to story, Lugia kinda got the shaft in the original gen II games. Thanks to HGSS though, we know a bit more about it. It perched on the Brass tower, and it's implied that its Rain Dance finally put out the fire to said tower. It moved to the whirl island afterward (note the singular term.) Then, when the island was under attack by two nations vying for it, Lugia split it into four (hence the plural) and basically told those humans to stay the fuck out of it because that place belonged to it. Lastly, I must stress this since there's no way around it: nostalgia. Pokemon Silver was my very first Pokemon game. Ever. Lugia represents my childhood in a way that not even Bulbasaur can. Nostalgia plays a part in my love for Lugia and I am not ashamed to admit it.