I think the only major issue of crafted gear being outright better than "rare" gear is in the case of weapons. For armor I was looking along the lines of say a Revolutionary's Bliaud vs. Vintage Robe (Looking only at Combat Stats):

Bliaud: INT+5, MND+5, PIE +5, Magic Acc +4, Parry +4

Robe: MP+57 MND +4

The Bliaud essentially has 3 more "Materia-like effects" on it over the robe. I'm guessing rare gear will be balanced so that It is more general purpose but better than what you could potentially get if you tried to make something similar with materia. You'd be able to make that vintage robe as good stat-wise or better than the Bliaud, but it would take a lot of time and luck. You'd need 3 materia attachments to make it comparable and a very risky 4th or 5th materia attemptto make it better. It also can be geared to be super specific (ie: instead of MND add more INT or Magic Potency to make a nuking piece). The balance would need to be that rare gear is powerful immediately and somewhat above the possibilities of materia, but it is not as "malleable" as crafted gear with materia set.