Eur-squee-ka!
Henry and Grace! (and no reprise of that cringe-worthy rotunda karaoke scene). Henry has been through the mill, so it's amazing to see him so happy.
Andy falling down a hole, and then falling over again! That never gets old.
Tess! (ish)
STARK! (ish) Seriously! I was wondering if they were going to bring him back for real, as he could be alive in this timeline, but I would guess not given the clues handed out in this ep. But still - STARK! Sunbathing on a rain-soaked bridge! (Ed, you are a trooper.)
Jack's Jeep. Oh bless him! Still, I can't help but giggle at the recurring joke.
Zoey! Still around. This can't be a bad thing.
Head Sixes all over the place, (I had made the connection already) and then that line from Grant about how his hallucination was "A leggy blonde, slinky red dress". Eureka, you WIN at BSG references!
Jo accidentally telling the real Zane about feelings, and please, please, please can this be the start of them getting together....????!!!! PLEASE!
Jack and Allison! Personally, I love them together. Maybe that's because I ADORE Jack and admire Allison and really want them to be happy together. Four years of textual unrequited desire - alternate timelines are good for this pair!
Fargo getting his bottle together. GO FARGO!
Beverly! Okay, I'm not a fan of Beverly, but she does make an excellent bad guy, so I'm quite pleased to see her. Also her reappearance may turn out to properly finish her storyline, and explain just who her associates are, and what they're about. Eureka needs something to be fighting against, other than the tech-gone-wrong du jour, and Beverly & Co are as good a target as any.
"New" Eureka, really is the epitome of "the more things change, the more they stay the same". It's the same Eureka, same-ish characters, same format of humour/drama/hurt/comfort, same plot formats with the tech-gone-bad and the awesome friendships, but with changes that they needed to inject to give the show direction. As great as season and 3.5 were, they couldn't have continued with things being as they were; there simply wasn't enough dramatic momentum to carry them through another season. So, yes, major shake-up, certainly more drastic than anything I would have done, but I think it's working for them, and more selfishly, it's working for me.
I'm sad for those it's not working for, but there's still seasons 1-3.5 to look back on.