Something is different about Emily, and it isn't the obvious.
Really look at her. Ignore the hair and the earring for now (though those are also big changes, they aren't the important part.) Why does her jacket look like that?
It's a standing collar, with an asymmetrical closure and a very square silhouette, even what looks like padding in the shoulders. It immediately made me think of millitary gear, and some very quick googling pulled up fencing style jackets that look almost identical, though Emily's is even more structured than these.
Emily doesn't look anything like an office worker anymore. The structure of her white shirt was very sharp and way fancier than anything her colleagues wore, but it was still recognisably office wear. Now, she looks like military leader, and the slicked back hair and cicular brooch like a badge or medal don't help matters.
This is a huge indication to me that the culture of the Oldest House has changed massively, and even personalities as sunny and excitable as Emily have been ground down by the constant fighting and neverending lockdown. She's the head of science, but unlike Darling's freindly and approachble lab coats and sweater vests, Emily has started dressing like someone whose orders are not to be questioned.
Really, the earring is actually the only sign that Emily is still keeping at least a little bit of whimsy in her life and self expression, but apart from that she is dressing like a completely different person - probably because she is. She's changed significantly from the character we saw in the last game, and I suspect the same is true for all of the returning cast.
...... and suddenly it all starts to make sense.
