Sorry if it seems like I'm posting too many crossover requests with this fandom right now, but I'm kind of limited in what I can post right now. There are only so many series that I know enough about to write ideas for, after all. I'll get back to Bleach crossover ideas when I can, but for now it'll likely lean towards the Fate series.
This idea is actually rather simple: have Emiya Shirou exist in the Toaru series, as a magician, utilizing tracing as his specialty. You don't really need to go into specifics on how he could possibly obtain all of the usual weapons he uses; just say that he studies old weapons in his free time, or something.
Have this Shirou be mature like the one post UBW, but not have actually experienced UBW; I do not want a pre-UBW personality Shirou running around in Academy city, as that would be counterproductive to some things I want out of this request. If you really want him to have actually experienced UBW, just leave vague hints to it having happened, or just in general work out a way for it to fit into the Toaru series properly, and then say it happened a couple of years before the canon story. I don't know what ages you might have to adjust for the characters to do this, however.
Basically, I want Emiya Shirou to help out Touma during his adventures in "A Certain Magical Index". He should be an active participant in all the various events that occur, and not just another character with a few scenes of dialogue every now and then. I want Shirou to rank as an unknown level esper-wise, because I don't think it'd make sense logically or to the other members of the cast if he were to be identified as a level zero with such an obvious ability available. If you want, you could even have the system scan malfunction due to his reality marble and label him as a level 6. Of course, you could also say that the system scan wouldn't detect the reality marble and maybe make him a level 5 due to his proficiency in tracing.
I also do not want Touma to lose his memories after saving Index. Have the events start diverging from canon early on in the story, and then have things snowball from there. This should not be a story of the same events occurring with an additional character. Don't put too much spotlight on Shirou; have Touma still be the main character for the most part.
I want both of them to have known each other since before they entered Academy city, and now I'll introduce one major difference from canon I'd like to see: Touma should already know about the "Invisible thing" prior to the events of canon, and he should have some amount of control over it without his arm being cut off. I think it'd make things interesting, but if you don't want to introduce such a concept then that works fine, too.
Touma should still not know about magic prior to the events of the story, despite Shirou being a magician. Shirou can easily write off his tracing as an ability that can't be measured by the system scan, though it would probably seem suspicious to most characters, or in the case that you made him a level 5 or 6, he doesn't even need to do that to hide that he's a magician, and there are no suspicions involved.
Shirou should, However, reveal his identity as a magician to Touma, no matter his level ranking, once Index is introduced to the story.
Do not add other characters from the Fate series to this story; I'd prefer it if it was just Shirou in an "Index environment", if that makes any sense. As I said before, there should be a number of canon divergences, and if you want you can even have it take a completely different route of doing things than canon. One such canon divergence should be that Shirou arrives to protect Index while Touma is gone, but she gets injured before he can arrive. Stuff like that.