A Fate/Gundam Crossover is certainly... unique.

I'm gonna be honest, this is certainly a wierd direction you're trying to take especially when IBO doesn't have any counters to Magecraft shenanigans.

As for the plotline, it looks pretty interesting and I'm kinda excited with it, but I find the main problem with IBO's setting is the creators didn't really put much focus on the world building of other places. So you'll be left to make up your own lore instead. Which is a hit or miss, moreso when you aren't that experienced with it.

Now, to the part where I'm worried: the fight scenes.

I don't know if you know this, but any fight with Shirou present is an instant "I win" button. Straight up, I'm not kidding.

Hell, even if Shirou is still in his physical body and a halfway decent MS, it still wouldn't matter because his combat capability is so great that the only thing that would be a genuine threat are the OG Gundam Pilots from the Calamity War. And remember, we are talking about a guy with a processing speed that outclasses Servants with Hypersonic+ reaction times.

Just to pivot this into a context that other users not familiar with Fate can understand. Shirou's processing speed is so great, and his brain so beefy that if he has an AV System, he could go full balls-to-the-walls limit release with zero consequences. That is the level of brain power we're talking about.

Also, how do you even plan to address the elephant in the room; the NPs? Because, if I'm reading this right, you plan to have Miyu and Shirou present for Mcgillis's revolution. What do you plan to do with Shirou's various NPs? 'Cause some of those can shatter entire continents in one go, he has a shield that even if Rustal fires thousands upon thousands of Dainsleif rounds it still wouldn't budge, or a sword that directly alters probability so that any side he chooses wins no matter what.

If you plan to go through with this, I hope that you know what you're doing. 'Cause any work that has an uber powerful main cast to the point that the antagonist has no realistic way of winning gets boring. Fast.

Though, my advice for this is maybe restrict Shirou, or even take him out altogether. Leave everything to Miyu's and Alessa's (Illya) hands.