The reason why it has a cost is IMHO just for balance: they did want the Wizard to have a cost when learning extra spells, they choose a cost in term of Gp and time (but for example not in Xp), and they decided to integrate the cost into the roleplay/flavor side of the game by saying it is spent for scribing.
I think that if they had chosen to say that the cost is spent in experiments to develop/learn the spell (which instead are costless or negligible) and made scribing itself costless, it wouldn't have change the cost obviously, but it would have had less problems.
Not just the scribing ruleset is messed up completely, but rather the whole spellbook thing!
Let's remember that by associating the cost for new spells to scribing them, for the Wizard her spellbook becomes a matter of life-or-death*: if it is stolen, lost or destroyed, you cannot really play once you have used up the spells still prepared (it's similar to the Divine Focus, except that it is much more difficult replace, and not all divine spells require DF).
Also, it was the cause of introducing the most no-brainer item in the game, which Boccob's blessed book exactly. An item which works like this: you pay some money to get a discount. Very clever.
If it was a feat it would be much better: you could choose between paying full price, or wasting a feat for a discount, but what sense does it make to pay Xgp to save Ygp? If X>Y no way, and if X<Y it is just a must have item, no reasons not to. Is this a proper strategic choice?
edit: *here I mean this... why the wizard can prepare spells only with the spellbook, while the divine casters can do it while naked and castaways on a desert island in the middle of the ocean, provided they have a comfortable hour of time? This could be the case even if the cost for new spells was disassociated from the spellbook, but still it is a thing that I don't understand why is here in the first place.