Sinnoh Mythicals:
Honestly, I'm kind of fine with how they handled the Sinnoh Mythicals and it feels like it makes sense why they're impossible to get:
Manaphy: First off, Manaphy isn't native to Sinnoh; it's not native anywhere. It's all in the Species name: The Seafaring Pokemon. Either it doesn't have a den or its den is on the bottom of the ocean. Eitherway, however Manaphy breed they do so in the middle of the ocean and sometimes an Egg gets lost and washes ashore somewhere. Thus why you can't get it in-game.
Of course, the argument
Yung Dramps presented is with the distribution method. And indeed, it sucks it's one per cartridge instead one per save file (and/or also make it so it cannot send a Manaphy to the same game file). I can sort of see their thinking, wanting to emulate an Event experience, but there's some ethics behind this which makes the whole thing icky and probably shouldn't have been done.
Phione: I guess the reason for Phione is to maybe explain how there's a Manaphy Egg when Legendaries don't normally breed. Now they could have just said Manaphy are picky about when they breed cause we've seen other Legendary's Eggs and/or offspring (or its mentioned) yet they aren't able to make lesser version of themselves; but I guess since you actually obtain Manaphy's Egg they felt this instance was different. Alright, fine, so, turns out Manaphy are the only Legendary to breed, BUT since they require specific conditions to develop into a Manaphy it results the Egg into being a Phione. Though you could just casually breed a Legendary/Mythical? HA! Shame on you, here's a Water-type Glalie for your efforts to play (or rather mate) God.
Honestly it's not a bad idea, but maybe not executed in the best way cause there's really nothing about Manaphy's theming which would make you think it could breed aside you normally get one via hatching a special Egg.
Darkrai: Why was it split from Cresselia? Because it's purposely hiding itself away from people cause it can't stop giving those around it nightmares, it doesn't want to be near others and doesn't want to be found. "How is that different from any other Legendary"? While other Legendaries like being secluded, they're not exactly opposed to be approached by someone "worthy" either because something is needed of them or the "worthy" wants to challenge them. Cresselia wings are able to give good dreams in addition to curing those out of Darkrai's nightmares, sure it lives on an island in seclusion but knows its power may be needed so does not opposed being visited by "worthy". Not so with Darkrai, "worthy" or not Darkrai wishes to be left alone. Why did Darkrai put Eldritch's son in a neverending nightmare? Who knows, lore seems to indicate Darkrai keep secluded because they don't actually want others to suffer yet such a life is lonely so once in a while a Darkrai may pull a victim into a neverending nightmare just to have a "friend" (though sadly the results look to be fatal if the ghost girl's story in B2W2's Strange House is anything to go by). This of course leads to Sinnoh's Darkrai event where, seemingly intrigued by the player who Cresselia considered worthy and broke his victim from the nightmare, breaks its seclusion and sets it up to meet the player. It's not the player going to find Darkrai, it's Darkrai finding the player.
Shaymin: Yeah, Seabreak Path is kind of silly and more GF showing off what they could do with the new tech as
DreamPrince said, but in Shaymin's defense it at least got a unique location to itself unlike modern day Mythicals.
Arceus: I mean, it's Pokemon GOD. You're same argument for why its presence is absent is also the explanation for why you don't encounter it. When was the last time you casually came across an avatar of God? Sure, you come across its children and other Legendaries that are nearly god-like, but Arceus is the very top, the Alpha, beyond you or me. You're going to be asked to be a bit more than just explore if you want to meet it, something that's beyond a normal player's control; an Event.
Though as I've said in the past, I'm all for them De-Mythifying Mythicals after their debut generation (or at least the majority of them, like Darkrai and Shaymin do really have no reason to remain Mythical).
Tropius has no variation as to what its growing, and it doesn't directly connect to any berry seen ingame (nanab berries are pink, for reference). Gen 3 did have a method for determining what fruit/berries a given pokemon likes, but still couldn't implement noticeable variants due to lacking a solid foundation for form changes (it had Spinda and Deoxys, but they were unique and not very generalizable). We're now at the point where everything is available for an interesting set of variants for Tropius or an evolution (and have potentially been since gen 4), and it would be far from the only mon nowadays with a set of different forms for a thematic gimmick. It means Tropius is now a mon that you can tell it's old without checking anything. It doesn't help that it hasn't been in the base dex for any non-Hoenn region where it might receive that update.
Well Tropius is far from the only Pokemon that has some fruit theme which doesn't relate to a holdable Berry. Cherubi and Cherrim has these pink "berries" they grow (Cherubi's has a face disturbingly, though dex says it eats it anyway), Applin family are based around apples which aren't considered a berry, heck, the fruit Tropius eats looks to be the same fruit for the
Fruit Bunch ingredient used to make
Tropical Curry.
Sadly, I don't think giving it a form change gimmick is really going to help it, it got a bad Typing and a stat spread totally unfit for it.
Here's a better question about Tropius: Why the F@#$ can it fly? Like, okay, I guess having a Pokemon use leafs as wings was the idea... but to make it a sauropod? GF, what media did you see a brontosaurus flying? Like, okay, I get idea of combining a long neck animal with a fruit-bearing tree, but to also combine it with a flying element? Felt like it was two separate ideas GF didn't want to make two separate Pokemon for so combined them cause banana tree leaves were long enough to be used as wings. Tropius could have been a Grass/Dragon than Grass/Flying; still wouldn't help it much but better than it has now.