Golden Girl

It'll be before then

Well, we don't know for sure yet who Primal Penny's mother is - although as she and Praetorian Penny both have huge psychic potential, the chances that Primal Vanessa is Primal Penny's mother are pretty good.

Mot is dealt with by the end of the DA content

It's not - otherwise, we wouldn't be sent to hunt down and arrest vigilantes in some of the missions

There's their argument in Fort Trident

Another thing this does is that it really ramps up the tension between Manticore and Penny - in the leaked part of the 2nd SSA on beta, his distrust of her as the newest member of the Phalanx can now be interpreted as partly down to the fact that her very presence there is a constant reminder of who she's replaced.

Well, Positron is replacing Statesman - a player-created NPC would replace Positron

I kinda think that intercepting an assassin before they get to the room where their target is is a way better thing to do that waiting for them to arrive

The comics and novels don't really matter for this - the SSAs and any other story content aren't being targeted at multi-year vets who have picked up a lot of the lore - these are for fresh players and VIPs too - people who will only know as much about the characters as the game tells them, because that's their only reference point for the CoHverse.
That's why the Phalanx are shown in the tutorial comic, and the tutorial itself, and why we get quite a bit of interaction with Manticore during Twinshot's arcs - since I21, there's been a big push to get more lore into the game, especially at the lower levels.

The feeling I'm getting is that the devs are going for something sort of like a "One More Day" style character reset for Manticore - they could think that the brooding loner vigilante with the tragic past role is a bit diluted by being happily married with the possibility of starting a family in the future - but rather than taking the "make-it-as-if-it-never-happened" route, they had him destroy the happiest part of his life by his own hand, which not only achieves the character reset, but also adds a fresh layer of personal tragedy, and in a way that players can experience the event.
Before, we just had the background lore telling us about the death of his parents being a defining event that helped to shaped his vigilante outlook - but now we have a new event that will shape his vigilante actions in the future, which we've actually seen ourselves, which helps give more depth to his character and motivations.

With her whole mind-riding thing, I'm kinda wondering if she hopped into Penny Yin's mind at the last minute, and will be "sleeping" in there for a while.

It might need to be in another zone - organizing your TF in Independence Port is eventually fatal

A leak from the 2nd SSA on beta says "no"

We should get a discount for making Super Pack threads in bulk.

It's shocking, isn't it?

When the sea gates open, she slips in under the hull of a ship

It'd need a good explanation - The Hamidon and the Devouring Earth are mutations of the natural world, sp they can be formed just about anywhere - Lusca can swim into the harbor from the open sea, and Jack and Eochai are from the spirit world of Croatoa which is encroaching on the town of Salamanca.
Eden was a normal part of the city until the first Rikti invasion 10 years ago - so there'd need to be a plausible reason as to how a breeding population of dinosaurs had ended up there - and when two different groups in the game already give players the chance to time travel, it seems kinda simpler to just make a prehistoric zone.

I think you'll find that quite a few players find the Incarnate system very entertaining

Can't they also just be traded normally?