Okay, laying this out in order of your arguments, some solid, some rather thin...
Dr. Awkward said:
The wizard and cleric should have a few Dispel Magics (or Greater DM) for just such an eventuality. They did realize they were up against a beholder before they kicked in the door, right? I generally assume that players will be at least minimally prepared for tough encounters, and spellcasters in my games know that without a good supply of Dispels, they'll have a much worse time fighting other spellcasters.
Show me the mage who can cast dispel magic in an anti-magic cone, and I'll concede this one in a heartbeat. Honestly, it's why the cone is -there-, to stop the be-all-end-all mage from being able to ruin the beholder's plans so easily. And if the beholder's aiming the cone at the fighter instead, or some other strangeness, then something's wrong.
Player: What was the spot check to notice the trap in the ceiling?
DM: Um... 50?
Player: Okay, rocks fall, we all die. Never thought I'd actually see that in a real game. Anyone want to dump this jerk and find a DM that isn't out to get us and plays by the rules?
Let's look at this one -without- the sarcasm. A simple trap door in a ceiling, even a jarringly obvious wooden one in a stone ceiling, has a pretty high spot DC in a dark-to-pitch-black 30' high room. If you have the dwarven fighter/rogue with the darkvision 60ft. in there doing his job, he points it out, and no big deal. You don't have to make a trap insane, simplicity and realism are good enough. Reflex save versus falling objects damage, equal to the maximum volume of the beholder's telekinesis. After all, if it's his trap, he has to keep reloading it. And if your party whines because the monsters can set traps, they should go back to smiting trolls. To say it in lolcat form: Intelligent monster is intelligent.
Assuming you're not just dropping the ceiling on the players without giving them a chance to spot the trap, but are actually trying to hit them with a thrown object, you must roll to hit. If you can't hit the wizard with a ray because of the Mirror Images, you can't hit him with a thrown statue either.
Again, anti-magic cone, Mister Wizard's Mirror Image (and mage armor, protection from arrows, shield, you name it) has gone the way of my cable during a hurricane. Lobbed petrified rogue has standard Telekinesis attack roll. May the gods have mercy on your AC.
Do most 9th level characters not have access to the Fly spell? Or bows? I notice that spells don't usually care whether your target is on the ground.
Most don't have flight that operates in an anti-magic cone...after the mage is toast, those repetitive 30ft drops onto broken masonry(see petrified teammates/previous parties) are going to feel alot like spiked pit traps till they get it through their heads that [5 ft. adjust back from meleer, slow eye/flesh to stone eye/disintegrate eye as free action, then turn anti-magic eye on him] makes for a bad day. And as for the bows, see Flyby Attack and other anti-will tactics, like beating the little elf ranger against the wall with telekinesis till you make the illithid in the next room sad you spilled his lunchtray.
Well, except for the rules.
"A beholder can tilt and pan its body each round to change which rays it brings to bear in any given arc." I'll give you that your argument on this one is entirely viable, as we're not clear whether this is the "up" of the battlefield, or the "up" of the rotating beholder. So, I'll leave this one to individual rulings by DMs.
So, they get +1 to hit and damage, and can fire into melee without penalties, as a solo monster? Wow, I can totally see how that could totally own a bunch of PCs. My apologies. It's definitely worth the -2 to Fort & Will saves.
+1 to hit is a big deal at times, but I'm really laying the groundwork for 1 HD of advancement. At 12HD, take Improved Precise Shot, and ignore anything less than full cover. If you're not going to do that, sure, keep the saving throw bonuses instead.
A prepared wizard should not be getting fried by eye rays, except if the dice go really badly against him. That is not to say that the rest of the party is going to do so well. I'm just speaking to the relative invulnerability of a reasonably defensive wizard.
A wizard should not be aimed at with eye rays, as they can't work in the cone either. He should be dealing with incoming halfling-shaped masonry. With all his "reasonably defensive" spells as useful as a paper bag in a blade barrier, he should be summarily executed with the swiftness, while the other eye-rays keep the rest of the party at bay. Then, the cleric, then, keep the fighter and rogue as pets as they should be perma-charmed till they get uppity, then beaten against the walls like ragdolls with the telekinesis ray.