Lugia is better off running whirlwind. Dragon Tail isn't breaking any subs thanks to lugia's downright terrible attack, while whirlwind, especially when used with substitute can prevent lugia from being set up bait for ferrothorn and forretress. Also, Lugia can shuffle teams very easily if its team has set up multiple layers of entry hazards.
Meh. Nitpicking. Whirwlind doesn't stop ferrothorn or forretress setting up on it btw. As soon as they're whirlwinded out, they just switch back in anyway. And if you're using Lugia on a hazard stacking team, then it's inferior to pokemon like Giratina-O, Ho-Oh, even Kyurem B pulls off a surprisingly effective hone claws dragon tail shuffler set.
Why the fuck does latias have more usage than latios? Because Latias checks Kyogre? so can Ferrothorn. Looks like we forgot about Soul Dew Draco Meteor off 130 spa. Latias is stopped by many more threats than Latios because of her much weaker offensive presence.
Because they do completely different things. Latias is an amazingly versatile pokemon, ranging from offensive pivot, to dual screens, to calm mind sweeper. Latios just blows teams to pieces with one very powerful set (I can't think of other sets it can do other than the 4 attacks wallbreaker better than Latias).
Seriously, use Latias more. It's so good. It does not "just" check Kyogre; it's an almost universal answer on the ladder to most Kyogre. Ferrothorn can only beat like, 3 of the viable Kyogre sets (Scarf, CM 3 attacks maybe, and maaaybe defensive Kyogre depending on scald burns). It loses to Specs, Crogre, CM+Water Gem, etc. Latias doesn't. That's not to say it can't be beaten, but on the ladder, a team with a Latias is generally safe from Kyogre. That is frigging
huge, ESPECIALLY because Latias is also a good pokemon, unlike Shedinja or w/e else.
Then there's the fact that Latias not just beats Kyogre, but also fucks with sun teams quite a bit (though lesser so now Genesect is a thing :/). Yes Latios can do this too, but only does it in one way generally, whereas Latias has the versatility to make switching in the wrong pokemon a game breaker. Switching in your Ho-Oh on a Reflect Latias can lead to a sweep from any number of set up sweepers in the tier. Switching in your Genesect on an HP Fire means dead Genesect (Genesect doesn't switch in on Latios for fear of this, yet on the ladder no-one suspects it on Latias, which is weird). Switching in your Arceus Ghost on a T-Wave Latias can severely cripple your main sweeper. Whilst nothing switches into Latios anyway, Latias has numerous common switch ins that can be taken advantage of in a way Latios cannot do as well.
And of course obligatory, "dat bulk", statement. It's the reason why Latias checks so much that Latios can't, making it an amazing addition for more balanced teams. Latias can withstand Ice Beams from Mewtwo, Latios is 2HKOd on the switch. Latias can switch in to Specs Kyogre safely (ish), Latios can't. Latias can take attacks like Darkrai's LO Dark Pulse and kill it or cripple it back, Latios can't (I've actually stalled out a Darkrai with Light Screen Latias before). Latias can survive Kyurem-W's draco-fucking-meteor if it fully invests, Latios can't. The difference in bulk is too great to even compare them in defensive utility; Latias simply stomps on Latios here.
Also I hate this implication that Latias is weak. Even though it can wallbreak to surprising success (I run a rain counter wall breaking set with like Thunder, Grass Knot, w/e I feel like), it's obviously weaker than Latios. That's just a tautology, no shit that a wallbreaker hits harder than a pivot/utility mon. But even with no investment, I THINK (don't pound me if I'm wrong) Latias hits 384 sp.atk. That is not weak. That hits harder than max invested Keldeo for instance. Its dragon pulses are only slightly weaker than say, Palkia's on average (it's like 1% or something).
So on review, you have several differences:
-Latias offers far more versatility and team support than Latios
-Offers near guaranteed protection against Kyogre on the ladder (I'm stressing this because at a tourney level it's likely to lose to some weird gimmick)
-Shits on Sun just as much as Latios, if not more if you're counter teaming with the set.
-Has far more defensive utility
-Can actually sweep teams as well as wallbreak (there's a reason you never see CM Latios)
-Still hits incredibly fucking hard if you invest
Yea, you really need to use Latias more if you think it should even really be compared with Latios. They're just different pokemon that offer different things, despite being very aesthetically similar.