Unova would likely getting my vote for a combination of well thought design and general charm. The tons of thought put into the box cover legends and the layers upon layers of ways their aspects and traits come together to make sense is really impressive, and the ways each mascot fits into its respective version gives me tons of appreciation for this group. All the neat ways intentional or otherwise that each Tao dragon relates to the pokémon exclusive to its version could probably fill an article on its own. The Forces of Nature grew on me after learning their neat relationship with certain Japanese and Chinese lore, and the Swords of Justice largely get points because of the general shortage of ungulate-like pokémon. Landorus is in the same boat here, considering it was the first tiger pokémon since raikou, and much more charming than inceneroar (I just like landorus's attitude, that "what are you looking at" expression is just priceless). Genesect's the first bug legendary, so it's got a unique factor as well, and while I kind of wish it had a more novel typing than the highly common steel, I still think it's an interesting point of speculation as to how it relates to other prehistoric or bug type pokémon. Victini's pretty well designed, and probably balances cuteness and coolness the best out of the legendaries (the thing's got the influence of a Greek goddess in its design and it's somehow still less girly than mew). And as for meloetta, I just kind of like it. It's got dainty charm and is cute, plus its pirouette form was a first of its typing.
I guess it's a wonder Hoenn wasn't my first choice, seeing as Hoenn is my favourite region, but its roster was likely a victim of circumstance. Hoenn was the first to really ramp up its number of legendaries, introducing double the number of them, having more uber-level legendaries than ever before, and being the first games that were impossible to complete without running into a legendary pokémon. You'd have to work to get the beasts and birds, while you were much more likely to meet a kyogre in the game than a chimecho, which I found a tad strange for such supposedly rare, mythical beings. That and it took me a while to have an appreciation for legendaries in general. The idea of a mighty figure with powers on the level of a pagan deity being possible for any ol' Joe to pop into a ball and take control of didn't sit with me when I was getting into pokémon (which was around the time of the 3rd generation's release). By the 5th gen, I was getting into classical mythology, so the references were more fascinating to me at that point. And while I'll always have a certain fondness for the Hoenn legends for their Hebrew references, the lore is a tad more tangential to their design than some other legends, and they generally come off a bit less personable with their more titanic designs. The two mascots do connect pretty nicely to the other version exclusives though, and they're second only to Unova in that, so with all that, Hoenn probably is a second for me.
With the rest it's a bit of a tossup. I can appreciate the first two gens' legendaries for being properly sparse and elusive, though monster for monster, those gens have fewer favourites of mine than some others. Sinnoh's a bit lopsided for me, as it's got some pretty cool real animal inspiration (bobbit worms and cliones!!), some really well thought designs (especially dialga, it's really cleverly crafted as a time beast) and some altogether charming pokémon (giratina is crazy awesome, and shaymin is just plain adorable), but the box duo doesn't resonate as well with the other version exclusives as the adjacent generations, and for every cool design, there's one that comes off a dud (the Lake Guardians probably represent the essence of the Go teams even better than the birds, and they still didn't get to be mascots, they're that forgettable). Plus, Sinnoh will always be remembered as the gen which introduced poké-god. As for the latest two, they're a bit recent for me to make a full judgement. Kalos's lineup seems to have gone for the short and sweet route, but after the big dump in Unova it kind of comes off as a shortchange, especially considering the main three come more resemble the more recent model of "two box bigshots and a third member tacked on", leaving the "sub-uber trio and little legend" that usually comes with that package conspicuously absent. The pokémon themselves are likeable enough though, and decently designed, and line up with the regular exclusives better than gen 4 at least.
Well, that's my super wordy opinion. Definitely likeable aspects in all generations, though some lead me to like them more than others.
