Ars Magica handles Dwarfism as a flaw and Giantism (Giant-blooded) as a virtue (feat).

Dwarfism makes it so that your size is -2 (default human is 0, things like horses are +2, a -2 size means you're, like, 2 1/2 feet tall) and you are wounded in increments of 3 instead of the default 5.

Giant-blooded is the exact opposite. Your size becomes +2 and you take wounds in increments of 7 instead of 5.

I think you should make Dwarfism a flaw and Giant-Blooded (or Giantism) a feat, both of which are exclusive and only can be taken at creation. I think that Dwarfism should decrease your size category by one and decrease your Constitution by 2.

Giant-Blooded should increase your size category and increase your Constitution by 2. However, that's a fairly kickass feat, so, it's up to you.