That's quite hard as I like all Pokémon so I will break break it down by generations.
Gen 1;
Articuno, I like his design and graceful he is. Plus I like how one of the binoculars in the gate separating Fuchsia City from Route 15 allows you to see him.
Gen 2;
Lugia, I love his design and I love his lore and how it's always on the back of your mind when you travel through Johto.
Plus I like how Lugia is aware just how powerful he is and hides in the ocean.
Gen 3;
Rayquaza, for me Rayquaza was this Pokémon that I was not aware existed even when I was playing Ruby as I never found Sky Pillar until I played the game the second time.
But the thing is the game hinted of a sky dragon flying in the sky and never stopping to rest which left me searching for the fabled Pokémon.
Gen 4;
Giratina, at this point I knew that Giratina would star the third version but what I didn't know what the Giratina in Diamond and Pearl was not its real form and when I saw its real form I was impressed.
I also love Sinnoh's lore but I also like how Giratina is the forgotten creation dragon as he was banished to the distortion world by Arceus for being violence but the thing is Giratina's role is important as he maintain the balance of antimatter.
Gen 5;
Zekrom, Like gen 4 I also loved Gen 5 lore and I loved how Zekrom was originally part of the original dragon but unlike Reshiram and Kyurem, Zekrom looks complete.
I also like Zekrom's design, its cry, its battle theme (though it shares it with Reshiram), but what I really like is that Zekrom represents ideal which appeals to me as I keep pushing myself to be an ideal Pokémon fan that respect other fan's opinions even if I disagree with them.
Gen 6;
Deoxys, now I know that you're thinking "Huh? Deoxys is a gen 3 Pokémon not a gen 6 Pokémon" But hear me out.
The reason that I chose Deoxys is because you can naturally capture it in the Hoenn remake and unlike gen 4 and 5 Kalos did not have a strong lore nor did they effectively use the Kalos Legendary into the story well.
Xerneas and Yveltal where thrown into the story and their role pretty much amount to them being used as a battery, meaning that they could have easily been written out and the game would still keep going.
Zygarde also suffers from this problem as he's just there in Terminus Cave and I was expecting his role to be expand in "Pokémon Z" but that doesn't seem to be happening.
Anyway back to Deoxys I like his design and I have always wanted to catch Deoxys in gen 3 but was unable to so I was glad that he was a part of Episode Delta and I hope that more event Pokémon get the same treatment.
I am already hoping that Darkrai gets the same treatment in the future Sinnoh remake.