I feel something like this should happen in the new game:
**NOTE** I'm unfamiliar with all of this CoroCoro, numbers and w/e crap, I'm going by my current knowledge of the new 4th(5th? Idk, I lost track after all of those other games like Ranger came out) Gen game.
I've seen a pic of the new Giratina and it looks pretty epic, I'll give it that. The wings do seem to make it seem faster or more fierce (as Dunsparce said, I do believe). So it SHOULD have a boosted base speed. I also agree that we should be able to capture Dialga/Palkia at a level higher than 48. However, consider why they're that level in the first place: Their rest (battle? Idk the movie threw me off on that one lol)was disturbed by Cyrus's activation of the Red Chain. So they were technically a pre-mature find. If Cyrus had activated the Chain later than he did (can't really give an exact time or date. That'd be extremely inaccurate), Dialga/Palkia would probably be at a higher level. Also regarding Dialga/Palkia, I think it should be something similar to Pokémon Emerald, where you can capture Groudon, Kyogre, AND Rayquaza in the same game (something similar to the "Mystery of Darkrai" movie, or whatever it was called).
Now regarding another legend/uber, whatever you want to call it is Shaymin. I keep seeing in this thread that Shaymin 'has another form in this game and we don't know if we're going to actually see this new form.' Personally, the only time I've seen the 'origional' form, as I'll refer to it, is in pictures outside of the games. Has Shaymin been in a game already (excluding using 'HAX')?
Looking at improvments within the storyline, I feel that something REALLY bad should happen, unlike in most of the former games. Oooooh the diety of space/time was yanked out of DIMENSION-X or whatever, big deal. It disrupted the Space-Time continuom for about five minutes. I'm looking for something more action-packed. Like, you're looking for Heatran and the volcano is shaking, and you find him/her, and after the battle whether you captured Heatran, ran, lost, or fainted it, the volcano should erupt, causing new Pokémon (such as Moltres) to be born or be able to be obtainable via Wild Capture. I say Moltres because I recall the Pokédex entry saying "Everytime a volcano erupts, a new Moltres is born." Well there you go, you've just unlocked a new meaning for the word 'chaining' in Pokémon. And even that could cause some sort of mandatory natural disaster that could last x-amount of time and its condition changes according to the time on your Pokétch, as long as the in-game event doesn't last freakin' 5 minutes like the Dialga/Palkia battle...
.::EDIT::.
Also, it could also be more like the 1st gen games (G/R/B/Y)and just be "I'm some 10 year old kid from a poorly named town in a country no one has ever heard of who wants to be the most epic Pokémon trainer EVER!!!"
Something along the lines of that would be just fine in my book :)
