If we're just going with the trend of the responses of judging the actual Pok?mon, it would be Blastoise, Ho-Oh, and Lunala as my favorites among them. I would also say standard Kyurem, but that wasn't a box mascot.
As far as the boxart is concerned though, I have a few contenders, those being Blastoise, Charizard, Lugia, Ho-Oh, Suicune, Xerneas, and Lunala.
If I had to narrow it down a bit, probably Ho-Oh, Suicune, and Xerneas. My absolute favorite would be Suicune.
My Thoughts on Each of the Boxarts Listed
Suicune: This one is the most iconic in the series for me. Crystal was my absolute favorite game in the series for years until HeartGold and SoulSilver came along and were just better versions of it (except for their replacing Kris with the inferior Lyra). I still have very fond memories of Crystal, and the fact that the Game Boy Color cartridge for Crystal was also a clear light blue was a nice touch. Suicune looks great on the cover and it stands head and shoulders over all of the others for me.
Ho-Oh: I initially preferred Lugia over Ho-Oh in my youth, but that opinion swapped as I got older and my appreciation for Ho-Oh increased dramatically. The covers for both the original Gold and HeartGold are great, though that older art style gives the original Gold the edge for me.
Lugia: In my youth, I preferred the boxart for Silver because I thought Lugia looked cooler. As I've gotten older, I've soured on Lugia's design because of its weird bulky hand wings. That boxart for the original Silver is still pretty striking though, so despite whatever my feelings are on Lugia now, it deserves the recognition. The SoulSilver boxart pales in comparison though.
Charizard: This is one of the more memorable and iconic boxart covers in the series for me. That classic art style just really looks great on the original Red version.
Xerneas: While X & Y are very easy games with little replay value, that doesn't change the fact that Xerneas just has a really striking design. It really fills out the cover and looks great doing it.
Blastoise: Maybe not the best boxart cover in the series, but Blastoise is one of my favorite Pok?mon and Blue was one of my first experiences with the series, so it holds a place in my heart.
Lunala: Not much to say with this one. I just really like Lunala as a Pok?mon and think it looks nice on the cover.