I think you'd first need to figure out what type of games you'd want this to be, and what roles do Ultra and other giant creatures play in it.
A game where you intend for players to be playing as either Ultras or other normal-sized characters would have quite different needs than a game where the focus would be only Ultras and gigantic creatures.
For the former type of game, because playing both sizes of characters is possible, the stats for both sizes would have to be built using the same "ruler" so to speak. In D&D terms, the system would have to be able to express your level 0 bystander, your level 10 SSIT pilot, and your level 30+ deity-level Ultrabeings. This makes the stats of Ultrabeings really bulky by default due to their immense power, but works without needing much adjustment to the D&D system.
For the latter type of game, as the focus of the game (or at least the combative, mechanical parts of the game) is only involving ultra beings (and perhaps vehicles), then we don't worry about the stats of normal-sized creature at all. Your basic Ultra doesn't need to start at level 30+ and be equipped with 100+ Strength to be logically comparable to your everyday pedestrian. Instead, your levels and attributes are relative only to other giant creatures, large vehicles, and Ultrabeings. This simplifies the stats and math of your character, although you'd need to make some changes to the D&D system.