I fail to see how this is an issue.

1: Obviously the OP is melding the materia themselves. Cause I don't see this atrocious despearity in odds (as I use NPC melding atm) - unless I'm removing it...but then im drowning in materia anyway lol
2: Materia Melds are based on Skills..... unless your using a melder (which costs gil...very little of it)

Conclusion - something is VERY amiss here.... makes me question the validity of this claim. @OP

And lets be honest here...if your burning that much materia to the point your getting mad over cost? You should have stopped at the 5th/6th attempt or something and got an NPC to do it for you.

Need more input :P