1) Could the giant skull belong to a sibling of Crossbreed Priscilla? Physically, there could be some similarities. She has little-bitty horn-like protrusions on her brow, and the skull has larger, full-on horns. In any horned species I can think of, the males have larger horns than females, if the females even have horns at all. A brother, perhaps? We'll come back to that theory in a bit.
2) The clams and the hydra seem to link Seathe and destroyed Oolacile (Darkroot) to Ash Lake. The only other place the clams are found is in the Crystal Cave. Maybe Seathe brought them back after a visit to Ash Lake? He's big on science experiments, perhaps he found them to be interesting specimens? Maybe he put them there? The hydra seems to be a possible link, too, as the only other one in the game is in Darkroot Basin, which has definite links to Seathe, what with the Moonlight Butterfly, the crystal golems and the whole Oolacile thing.
Why would Seathe go to Ash Lake? For the Stone/Everlasting Dragon, maybe? Perhaps he (and maybe the gods also) got wind of a surviving dragon and went to investigate to try and obtain some Dragon Scales and kill the last dragon. Maybe then a fight broke out between Seathe and the Dragon, or at least it's servants, hence all the corpses with Dragon Scales. Maybe the giant skull belonged to Priscilla's relative, who went to warn the Dragon of Seathe's approach, or even protect it? The gods killed off the dragons, so perhaps this guy was killed for trying to warn the dragon and Priscilla was punished for her relative's transgressions against the gods by being banished to Ariamis.
2b) Havel is linked somehow to Ash Lake since one of his miracles is found there...Perhaps when he heard of Seathe's movements against the dragon, he saw an opportunity to strike against his sworn enemy.
Text from Great Magic Barrier:
"Havel the Rock, an old battlefield compatriot of Lord Gwyn, was the
sworn enemy of Seath the Scaleless. He despised magic, and made certain
to devise means of counteraction."
Since Seathe helped the gods defeat the dragons, maybe this is why Gwyn had Havel locked away, as punishment for fighting Seathe.
3) The broken tree could have been destroyed in the fracas. The mushrooms seem to me to be offspring of Elizabeth gone hollow, or maybe even not hollow, but just doing their job. They only pop up in Darkroot in our time and Ash Lake/Great Hollow. I think they're definitely linked to Oolacile and Elizabeth. I was thinking that maybe Elizabeth's children were trying to restore the Arch Trees, but then again, mushrooms don't exactly repair things in nature, they break things down. Something's up with them, though...they're also protecting the Enchanted Ember, which is linked to Oolacile.
Anyway, I see Ash lake having strong ties to Seathe, Oolacile, Havel, and maybe even Priscilla with that giant skull. What say you?
edit: Heck, now that I think about it, maybe the Stone/Everlasting dragon is Priscilla's father. He can't be killed (that we know of. I, like others, have my doubts), and she has powers that drain life, so there's a "life" connection, weak though it may be. Maybe the skull belonged to junior going to protect daddy?