[...] if the DM is now just changing the rules because someone knows how to zone their enemy [...]
There isn't any such thing as "just now changing the rules" for a GM. The GM is the first and last call on the rules at any point in time.
If players extend the game into areas not covered by the rules, the GM has to make stuff up to handle it. Calling BS on a GM when he is working to handle non-standard situations is just ingratitude. GM's aren't perfect. If things go badly for a player as a result of an off the cuff GM call, that's the way the cookie crumbles.
There is difference between random decisions on existing rules and needing to make up rules that didn't exist until that point in time.
And the second or third time a boulder appears in midair,
The spell being mentioned is Invisibility. The moment you roll the attack to hit when you drop the "shrunken boulder", then as long as there are any foes down below, which seems likely during a siege, the attacker becomes visible. You would need Greater Invisibility to get past that, which requires a higher-level caster. Higher altitudes introduce ever-greater winds for extra to hit penalties.
The SRD's array of spells really have little or nothing to do with siege warfare. While there are plenty of spells that appear to cleverly aid an attack, there are few that appear to assist in defense, at least for long enough to cast ahead of time and without xp expenditures.
This subject has been debated going back many years. What if your enemy builds not traditional medieval castles, but cubes ala Barbara Hambly's Time of the Dark? Dropping rocks on that is going to be pointless. The entire structure is enchanted. You say that is difficult and expensive? Yes. It also laughs in the face of its enemies. In a magical world, the castles are going to be enchanted to one degree or another in my opinion.
Then there is the old "city of illusions" trick. The enchantment that goes up makes it so that people who approach the castle cannot find it unless they are guided in by the inhabitants.
There would probably be a whole sub-profession of Wizards that works on fortifications.
Walls of Force (the spell) can only be cast vertically.
There were interpretations where older edition versions could be cast horizontally.
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In 3.5, a Wall of Force is 10' x 10' per level and a Permanency requires 2,500 xp per spell. To cover a castle (or what comes to mind when I think of castle) would require a huge amount of xp. That amount isn't going to be readily available for any amount of money. So, even beyond there being no horizontal casting in this edition, it seems unlikely it would be used to defend a castle, at least to me.
Bah! See invisibility has a range of personal, your town watch would have to be composed of 10th level wizards
What does a range of personal have to do with being a 10th level character? In 3.5, See Invisibility allows: "You can see any objects or beings that are invisible within your range of vision [...]" The spell has a range of personal, not the vision granted.
See invisibilty doesn't come up till the rocks start falling.
The falling rocks have no bearing on See Invisibility, unless they have been made invisible somehow, in which case See Invisibility will allow them to be seen.
Why not just teleport over the target with a shrunken mountaintop,
By what means is the mountaintop being shrunk? The Wish spell?