-The elemental Cosmo (granted, they started ignoring it half way through S1)
-The relationship between Kouga and Yuna got reset.
-Ichi's Hydra Bronze Cloth looking like the original version, even though we saw the Clothstone gauntlet back in ep4.
-Ikki's Cloth.
-Tokisada's death.
-Silver Saints' deaths.
-Eden now being a demi-god.
-The elemental cosmo wasn't important even in season 1, and basically outright disappeared in the Twelve Houses, apart from Light and Darkness (the latter of which does get referenced in season 2).
-What relationship? They haven't ever been more than friends. If you honestly think more than that...you might want to get those shipping goggles off. Better for Kouga this way anyways, Pegasus Saints have a HORRIBLE track record with relationships...
-Ichi's Cloth might've (de?)volved between the seasons. When Kiki repairs it, the Hydra Cloth has a physical form, so it's clearly not a Clothstone anymore. Hilariously enough, this would mean that the first person to make his Cloth evolve from a Clothstone is
Ichi of all people.
-Supplementary materials point out that Ikki's Cloth actually returned to its original form, so it's not a retcon. Nonetheless, it's not explained why, but it might've been because it evolved from its Clothstone form by reviving Phoenix-style, rather than getting repaired or using Athena's blood (which it has, but...). In reality, though, the Phoenix Cloth using its Hades design is clearly for the fans' sakes, since even the New Cloths haven't been well-recieved by everyone and Ikki is ridiculously popular (and the series treats him like the best Saint ever, not like anyone's complaining).
-We're never told Tokisada died. We see him getting lost in time, so what happens to him is near-perfectly possible (the only actual hole is how the Aquarius Cloth returned from the edge of time, with the only possible explanation being that Tokisada sent it back himself...which makes no sense)
-I have no idea about the Silver Saints, I noticed that too. Perhaps they didn't really die, they were just left for dead. In either case, they've been absolutely unimporant (which is still a step up from the usual Silver Saint treatment of getting their asses kicked repeatedly like the cannon fodder they are), so...
-Eden was a demi-god even in season 1. It just wasn't really important because his "job" in Mars' world was as its ruler, not as a God.