I'd say you stat the Gundam up as a character in its own right. I don't think treating it as an Item of Power is really sufficient (and thematically it is kind of weird). Something more construct-like makes more sense. There are a number of good reasons to do this. First, you aren't a joke when you don't have your gundam or can't use it (like gundam pilots, you could still kick some ass well as a Pure Mortal). Secondly, since the size difference is so large, a gundam is going to be something encounters are going to have to be designed for anyway (either assuming you have it or assuming that you don't), and you might as well treat it as something different at that point. Note, this means that the gundam can be upgraded separately from your character and vice versa without creating an odd cost-benefit analysis. Lastly, unlike the average item of power, this isn't something you can carry with you 99% of the time so being an external item is a much bigger deal than the Item of Power rules were designed for.
Now granted, some things are going to have to be adjusted for a gundam. Skill use and so forth would need some custom tweaks (using the character's skill for some things like Guns and Weapons), but overall the benefits of treating it as a separate character outweigh the penalties (heck, the gundam could potentially have its own Trouble and other aspects that come with it when you use it, which might fit the campaign very well).
