I always do the regular brushables, which are 3.25 inches tall. I mainly customize them because I want them to blend in with my collection, which is all that size.
There's also the added bonus that it takes less time to rehair and your doll hair will make customs of a lot more ponies that way! On the downside, their butts are pretty tiny, so painting their tatts is that much harder (and I'm already not that great at it).
If your friend already has a collection, you might ask what size he collects, and whether he wants all his ponies to be the same size. Remember, the smaller brushables require less time and less hair. However, as has been stated, you can get better painting detail on the larger sizes, so the final product might look a little more impressive.