Okay, I'm 50% confused and 50% disappointed.
Let me try to figure this mess out for myself...
So, in PokeSpe, Sinnoh and Johto are not geographically close to one another and are just simply linked by this inter-dimensional crap? Or are they still close to each other and this dimensional area is there anyways?
Pryce explained that the Sinjoh ruins do not really exist in the real world. Rather, it exists in an alternate dimension that links Sinnoh and Johto (which is why it appeared mapless on the Pokegear, I guess you can think of it like the Hall of Origin at the Spear Pillar).
... *facepalm* Pich really did nothing outside of become a catalyst for the appearance of the movie-promoting rodent. Cerebi could have retrieved the herbs to heal Giovanni off-screen and it wouldn't have made any substantial difference to the plot.
While everyone was fighting at the Sinjoh Ruins, Celebi is actually finding the herbs and meds to cure Giovanni with the help of Gold's Pichu (don't ask me how, maybe through Oak?). Spikey-eared Pichu appears as a wild Pokemon, became Pich's friend and the two work together. Ken, Al and Harry are protecting them, but then a group of TR Grunts working under the Four Generals thought that Ken and co. are disobeying the Generals, and thus attacked them. The two Pichus fried them with their electric attacks.
"Silver, I want you to study under the supervision of the guy that kidnapped you and a bunch of other kids!"
He offers to let Silver join, but Silver decides to continue to mission to disband Team Rocket with his own hands. Giovanni accepts this, and wants him to become stronger under Lance and Pryce, his two former teachers, and come back to challenge him some day
...Smooth one, Giovanni.
THIS. I think I can make an accurate guess on what Kusaka's favorite legendary is.
Pryce being brought back by Celebi is a bit weird though, and its kind of annyoing that Celebi has become the all mighty fixer of time. Your not doctor who, your a green fluffball that can time travel, stop fixing things.
In regards to the timeline, it shows that absolutely anything is possible. This also leaves a three-year gap in the timeline since nothing is known to take place between Emerald and HGSS.
I also formally withdraw my theory that the next Dexholder reunion will be in BW2. It would be awkward as hell and probably wouldn't work out anyways. Unless, against all odds, they release some more remakes I cannot see any previous Dexholders from Gen I-IV appearing (outside of a remark in passing or even a brief cameo).
I think DreamingFlower best summarizes how I feel about the HGSS arc:
I know I'm getting a lot of my facts wrong in this post, but I really couldn't give a flying **** at this point. In my opinion, the art was good but the writing wasn't. I know Kusaka can do better than this.
I feel like pretending that the whole HGSS fiasco never happened.
HeLlO. You'Re tOo slOw. yOu cAn'T ruN. FOuNd YOu! I AM GOD.