UniversalWolf: If you consider a wizard with a meagre CS of 60 or so depending on book selection, that's enough to cast Flamestrike, so he can do so in as many battles as he has to fight during a single turn as long as he has the crystals. If the rule worked the way it should work, he would have to be judicious about casting Flamestrike, because he could only use it in one of the battles. That's reason enough right there for it to work the way it should instead of the way it does.
The way it works now makes the most overpowered spells even more overpowered, and decreases the need to think strategically about how to use all combat spells in turns with more than one battle (and you never know for sure when you might be surprised by a battle you didn't expect).
Why should your CS replenish after a battle, anyway? Does your wizard chug a bunch of mana potions or something? Then why can't he do that for artifact creation?
I'm with TwoHandedSword on preferring that each battle gets your full spell skill.
On the technical/rules side: He's already mentioned the AI abuse (the AI already can't handle of lot of things well, and the level of planning required for anticipating what battles will be fought in a turn AND planning what spells you might need in those battles is crazy high), and getting jumped by unexpected battles in a turn where I have other battles planned (or see the risk for them) is exceedingly rare. There are just too many ways to see things coming (like spearman on patrol, if it were necessary), with the main exception being units (like new spawns) using enchanted roads to move a long distance. You are still limited by your stock pile of mana crystals; I don't know about you, but I'm usually running a fine line of "just enough mana crystals to get me to next turn without losing anything while I cast my full spell skill overland". I tend to run 0 mana income (putting it all into spell skill), and so gold/mana management is a big issue in my early/mid game, especially when I have overland spells I need to maintain. There is also the casting range multiplier eating into your mana crystal supply as well.
On the flavor side: one explanation for why you get your full spell skill each battle comes from the complexity of overland spells versus combat spells. Generally, combat spells will be enormously easier to cast than overland spells because of the scope of effect. Setting up a wind of death that will sweep across both worlds just sounds much harder than putting a unit into a temporary coma or throwing a blast of [element] at it. Creating a holy armor spell that will pull power from a battery (your mana supply) and last as long as it has power would be harder than throwing enough power into the same spell to make it last a day (or even an hour). The amount of mental involvement is much greater in creating a permanent magical item than in summoning a magic being that only needs to last for one battle.
All that said, maybe you just need a few minutes or an hour to clear your mind of the battle you just fought, and put your thoughts in order (or, on the flip side, you take a few minutes to prepare yourself for a series of rapidly cast spells just before each battle starts). Your spell skill in general reflects your ability to manipulate the fabric of magic in the worlds, so a wizard with more spell skill is just better at putting spells together, both overland and in combat.