Personally, my issue with Emerald’s version of the scenario is that it’s kind of a hackneyed deus ex machina. First, the game steers you toward the Sky Pillar in the most abrupt way possible: Wallace reveals out of the blue that a third super-ancient titan exists. Then, for some reason, the Champion of Hoenn has to ask you, a literal 12-year-old who has never heard of the Sky Pillar (unless you already played RS), where you think Rayquaza is.
Yeah, the Wallace bit is... weird to say the least.
Since there's nothing stopping you from going to Pacifidlog and the surrounding areas, my assumption was always that the game devs assumed that you would have already explored the entirety of those southern routes and come to the Sky Pillar before meeting Wallace (perfectly possible to do, but the door's locked) thus making it plausible that you would know of it and be able to recommend it to him. Otherwise it's nonsensical, because the options are "don't know", two places you do know, and a third you don't.
Of course, this is due to the fact that you basically have free rein to do what you want once you're able to Surf beyond Lilycove, something RSE is fairly hands-off about. Much as ORAS tweaked things so that you were railroaded into beating Winona before being able to proceed beyond Fortree, I imagine that a hypothetical Emerald remake would have necessitated the player to complete some sort of mission in the vicinity of Pacifidlog as a condition to gaining access to Sootopolis/Seafloor Cavern. Or at the very least heavily hinted about it so that you at least knew the name and could go "oh, I've heard about another location..."
Once you’ve process-of-eliminationed your way through the set of options that the game inorganically provides for you, though, you as the player don’t actually do anything significant. You don’t overcome any noteworthy environmental obstacles — the Sky Pillar is still in a pristine state where you can simply stroll up to the top. And you don’t battle anything or anyone important on your way to Rayquaza. All you’re responsible for is tapping Rayquaza on the shoulder and saying, “Hey can you go fix this for us? Thanks.” And then it does, magically, with a single roar. Kyogre and Groudon shrug and leave. The villains dutifully repent. Everything’s fixed now. But none of this was earned.
Yeah, can't argue here. What's weird about it is the Mirage Tower was seemingly created as a practice round for the Sky Pillar, since it has the same basic puzzle, so it
would have felt reasonable to progress through a gauntlet.
While I appreciate the little implied detail that apparently Rayquaza landing on the Sky Pillar once it returns apparently shook the place badly enough to cause damage to the place and crack the floor, it is dull that the location is so pristine on your first visit. Perhaps they thought the puzzle was too difficult for most people, since it takes some quick finger-work to zigzag around some of the corners without falling. Maybe they just thought it'd be boring to do the same thing twice if you want to return to catch it.
I don't fully agree that it's dull to awaken Rayquaza - I remember being quite awed the first time I played, and there's a definite sense of "what's going to happen now?" when it flies off. Sure the climax is a bit abrupt and the return to clear weather is very quick, I wish it had gone on a little longer. But you have to consider the context: at the time that cutscene was very impressive by the standards of what had come before. It wasn't the fully realised 3D scene the trailers displayed, but Pokemon's visuals have never been that spectacular. I recall a friend once looking at my DS screen and saying "the graphics are incredible" in hushed tones when DP came out, which... sure.
And I actually really like the way Archie and Maxie's repentance is handled. Wallace says it wouldn't hurt to hear what they have to say, but I didn't get the sense that all's well and they're completely forgiven; it's more that everyone, them included, fully agrees they've been stupid and reckless and they need to make amends. Their goodbye scene at Mt Pyre indicates to me quite strongly that they're going to be spending their time making amends from here on out (fun fact, I used to determinedly avoid ever doing that sequence whenever I played RSE as I found it incredibly sad).