In the traditional FRPG, the setting is a medieval time period, with, of course, various monsters, and magic. In this world there is war. Of course there is war. There has to be. There will always be two countries who just can't get along, or a country that thinks that that bit of land would look far nicer under my control, or a country who thinks that this and this god wants this and this country gone. And as is always the case, countries pick up sword and shield, ready the trebuchets and catapults, and head off to either unimaginable heights of glory, or a close up and body-less view of foreign grass (and usually a fair bit of blood, intestines, brain matter, bones, etc, etc). This is all well and good, except for one crucial detail: magic makes everything obsolete.
The first thing that we shall look at that is obsolete because of magic is the wall. In the real world, the wall was a very tough thing to get past, up until gunpowder. But this is fantasy. In real world, everything is, more or less, two dimensional. There were no flying contraptions to simply fly over your wall. But in fantasy, there are. It is called the wizard. A sufficiently leveled mage gets access to the 'fly' spell. And then they can fly right on over that 10 foot wall. Its only the everyday fighter who has trouble with a wall. But wait- whats this? A potion that allows anyone to fly? Preposterous! That would mean that those everyday fighters could get onto the wall, butcher the archers, and open the gate! If any city wanted a wall to protect against flying people (or people riding things that can fly), they would have to put up the expense of building a dome. And ignoring the fact a dome would be next to impossible with medieval technology, when the city expanded (which all cities do sooner or later), they would have a Problem. This Problem would take the form of to little money in the treasure because of the expense of the first dome to build the second.
The second obsolete thing is the siege engine. Or rather, next to obsolete. There is still room for the siege engine in warfare. There are two main types of siege engines: the ones that get up real close, and the ones that stay out of range. The first type consists of siege towers (the main idea being a tower on wheels), and battering rams. The ram is now obsolete. Say goodbye to it, and say hello to everyone's favorite spell: fireball. A couple of fireballs would do the same work as a couple of swings of the 'ol ram- more efficiently. Because during sieges, boiling oil would generally be poured onto the people swinging the rams, that would mean to things: no more ram, and no more ram-swingers. On the other hand, if one had a handy siege tower, put it over the wizard, then the wizard would be protected as he turned the gate to dust, random frog, giant monster, or ashes. Of course, the siege tower could also be used to house archers and wizards towards the top, to kill a few of those pesky enemies on the walls. This would mean that the siege tower is still useful. The second major type of siege engine is the out of range type. This includes catapults, ballista, trebuchets, etc. Each of these are powerful tools. There one advantage over the wizard is range. A wizard, generally, has to be within range of the enemy (except when flying- arrows can't go as far up as magic can down. Its called gravity) to work his spells. A trebuchet does not. But the thing about the wizard is that they, if alone or surrounded by a meatshield, hard to hit with arrows. Whereas spells generally are on-target. Added to this is magically enhanced siege weapons. Catapulting a rock is not as effective as catapulting an Earth Elemental, which would both smash the wall on impact, and then stand up and continue smashing walls. Or you could catapult a magical explosive. And you could give a trebuchet a much heavy weight, while making the ropes and wood next to impossible to break.
Another obsolete aspect of conventional warfare is the technique of starving of the defenders. In the real world, the besieging army could simply close off trade routes and wait for the enemy to run out of food (hopefully before you do). This, too, is pointless, if the defenders mage cannot teleport. If they can, then they can simply teleport to on of their allies, get a sack full of food, and teleport back. The same thing can be achieved if you have anyone that can magic up some food or water. The same technique can be used to aide the invaders. The invaders main food source is anything they can pillage from nearby towns and villages. Once this runs out, they would normally be forced to either make a last ditch attempt to take the city, or retreat. With magic, this problem goes away. The invader's wizard would simply teleport back home, or to an ally, grab some food, and go back.
But there are ways to stop magic. This generally involves more powerful magic. To stop people flying over your walls, the creation of a disspell magic field works. Of course, then the enemy wizard would, if he/she was more powerful then your own wizard, get rid of that field. The same applies to wards on your walls, etc. This would turn a siege into little more than a contest toe see who has the most powerful wizard. The person who did would, probably, win. If the attacker had the most powerful mage, then they could do everything written above- fly soldiers over the wall, turn those walls to smithereens, etc. If the defender had the most powerful mage, then they could remake the walls every night, hurl fireballs at close nit enemy formations, etc. There would be little to stop one side's wizard from dominating combat.
So how to stop magic from overturning conventional warfare? One way would be through something like a Geneva Convention. All the prominent countries get together and agree that magic should be left out of combat, and keep it to healing, and they ally to make sure everyone agrees to such this. Another way would be to make wizards to proud to fight. To proud to sell their magical talents that they worked so hard to develop go to the highest bidder. To proud to sell the spells they researched so careful, pored over so many books to find. To proud to decimate entire army corps because some idiot meatshield fighter said so. And there are other ways. Whether or not you actually use magic in your wars is up to you. But if you do, then make sure that those wizards use it smart. They might not feel that several fireballs against the wall would be as effective as simply turning the ground beneath it to mud (which would, of course, collapse that section of wall). Magic in war is not something to be used lightly.