Okay, I will try to make the other sprites, but it might take some time, because I'm very busy at the moment (school, work, friends...) but I think it will be done in time. Thanks.
I have some story ideas to.
First Celebi: Like in japanese Crystal (get GS Ball in PokeCom Center after E4 then go to Kurt and afterwards to the forest shrine) Mm-hm. Except, with the Global Trade Server being down, something slightly different will cause the ball to arrive...
Legendary Birds: Like in HG/SS (because Red did not catch them in the GS timeline) No. Just no. This is a bad idea. Like somebody else in this thread said, it was like they hadn't moved an inch for three years. So no, you will get them, but not like crappy HGSS did it.
Mewtwo: Also like in HG/SS (for the same reason) See above comment.
Mew: when you catch/defeat Mewtwo you find a "Myterious DNA String" you take it to the fossil researchers (also like HG/SS) and one says that it's from Mew, then he remembers the "Old Sea Chart" they found in one underwater expedition and gives it to you, so that you can find Mew (than it's like in Emerald). Nope. It's already been planned out. I'm also thinking of doing you a better Mewtwo OW so that Mew's isn't bigger than Mewtwo. Thanks, I'll need that.
Ruby: Since Ruby and Red had their adventures at the same time you could put Ruby into the game to, only that he is in the Seviis istead of Mt. Silver, he could have a team oriented on the Hoenn Starters Gardevoir and two others. Maybe. If I do, however, it'll probably be a double battle between the player and Silver against Brendan and May (or you and May against Silver and Brendan, or another arrangement).
Regice: in a new chamber in Ice Path after defeating Ruby Sounds interesting. Come to think of it, I still haven't done much for anything from RSE...
Regirock: in Rock Tunnel after defeating Ruby Makes sense.
Registeel: Somewhere in the Seviis after defeating Ruby But the other two are in Johto, aren't they? How about, maybe, Mt. Mortar?
Lati@s: Roaming Kanto after defeating Ruby No, too much like HGSS. They'll probably still be roaming somewhere, just not Kanto.
Groudon Kyogre Rayquaza: You find the Ruby and Saphire on the Seviis. After you give them to Celio he thanks you, because he lost them and then tells you about Groudon and Kyogre which are said to live under the Seviis, because they departed from Hoenn after the Big Battle they had three years ago, he then gives you the ticket to Navel Rock, where you find the two (both in underground Caverns) When you return outside Navel Rock collapses and on your next visit you find the Emerald! You then show it to Celio who then uses it to improve the Link to Hoenn, but something goes Wrong and you are teleported to Sky Tower (you can't leave because the Cave to Lillycove has collapse in the past three years) here you can catch Rayquaza, after the battle you are teleported to One Island again, where Celio tells you that Rayquaza may have wanted you to Tame Groudon and Kyogre once and for all. Some of what you said is actually what I'd already planned out! But the whole teleportation to Sky Pillar thing, how you find the Emerald, and some other things will be different.
Deoxys: After defeating Ruby you find a strange meteor on Mt. Moon Steven Stone meets you and tells you that something is not right about the rock he than gives you the Aurora ticket, because he thinks there is a connection between Birth island and the meteor. (I can make you a FR/LG Steven Stone sprite too ;) ) Yeah, go ahead and make the sprite, that would be great. But Deoxys will probably not be on Birth Island.
Jirachi: After defeating Ruby and returning to the place he was on the Seviis (It has to be on a mountain) and it's night you find a strange Stone where a writing is carved into which says that you should make a wish which comes from your heart, after answering the wish Jirachi appears (I will try to make sprite for it to) Thanks for the sprite, but I think I just might make the event, whatever it is, happen in a special little place on Mt. Moon...
Hope you like my Ideas for the Legendaries and maybe implement them ;) I like some of them, but the others are not what I had in mind/already planned out.