Go with crosshair. Though that is incredibly unbalance, fun, but unbalaced. Even if it cost 999999oz you still get the ability to ingore landing zone and instant strike on enemy's brain. Leave it for cheat mode that you have to comment out, maybe. I agree with someone before, that it should be a gun/portable targeting computer firing out a crosshair, and there should be a timrer that says how long can you still control it, to limit the range.

Now for the attacks. Since everyone's thowing out ideas of attacks straight down from the ship, I'm only gonna think of some non-linear ones.

Iron Maiden Strike:
Select a target. A tall tower-like structure/device with drop from the ship, securing itself on the ground. Which then releases a barrage/wall of spikes to sadistically kill nearby enemies, thus the name. The Maiden will scuttle or turn into terrain. The spikes left can be used as covers.

Forcefield Geneator:
Why not? Every spaceship can beam down one to protect its troops. Either a beacon, or and instant shield made on target spot.

Chemical Warfare:
A rain of gas grenades coming down. Or a big bomb that releases toxic goo.

Electro-magnetic Disruption Charge:
It is dropped, and releases an EMP field, trapping enemies inside. Then a countdown will start, showing how much time the poor guy(s) in there have left, before a deadly electric discharge which runs throughout the field fry them all. It can only be disarmed by units not caught in the field. (And basically the trap ones act as hostages/human shields)

As for the drop system, it would be plain to just drop stuff. Maybe a rocket frame that delivers these stuff, and returns to orbit. The Kloveska droppod is something similar.

A ODST type droppod loaded with a infiltrator pilot(or something like that) would be useful between ion cannon reloads.

Having a mini-Railgun to snipe (and gib?) single targets would be good too IMO.

How about an exploding laser swipe? ~200px to the left or right of the target (I prefer TDE beacon, but painting is cool too, crosshair thing sounds tedious) the beam starts, sweeps across to ~200px to the right or left, then after a few seconds giant pillars of fire/plasma erupt, spewing pain skyward and sideways.

GDI Ion Cannon.

Have a 25 pixel wide beam fall from the sky for about a minute.

Make it a dreadnought, many turrets, a few actor docks, and shields.

Either that or make it an A70M1C Vault, it constructs itself slowly, 'incubates', then it releases many demons, or a really big one, here are four examples: Vault 17, Epic 17, Vault 99, Epic 99. ( Be wary these are YouTube Videos, and you may need to attach turrets )

scrap that a bit. The main ship has turrets on both sides comparable to the small Darkstorm turrets strength but are vary durable and every now and then a random homing rocket is launched and after they are destroyed the droppod deploys, the ship becomes immobile and a timer starts(say 1:30) after the timer ends the ship auto scuttle's REVILING THE YPSILON CANNON but now it doesn't stay in one place it scrolls across the screen horizontal not damaging terrain but killing EVERYTHING unless it is destroyed first(Ion overload blast of rap or the compressed ion power shred a hole in space in other words blackhole with the normal boom?) and after it runs out of fuel it crashes with a average blast but with lots of little killing gibs! Not only does this make it useful and powerful but not overkill! if troops are on the surface they are in trouble with the turret gun and the few homing rockets but when there destroyed they can try to kill the ship unless the droppod troops kill them while defending the ship and a few could go clean out the bunkers a bit,then of course the beam and crash are just not a good thing to say the least!

and I know it says we shouldn't see the ship but were is the EPICNESS and danger of that!

The target/cursor would look awesome if it looked something like this.

A singular powerful beam that quickly expands, becoming an extremely weak but spread beam. High damage in the centre and decent damage over a large area.

something of the same style, controllable, fired with a button. none of this crosshair crap. have the superweapon come to you, and make it awesome to take down.
also, make it so all the weapons are charged with lua timers and use bars simmilar to darlos's shields, with their own little icons. i think it should have lots of weapons, as well as the final stage.

MAIN WEAPONS - mounted and powerful.
-an ypsilon style beam that didnt rape terrain too hard but could open up a bunker (should have a long recharge), with some residual lightning effects, and a kinetic shockwave (lua based mopixels that push away actors) *BOOM* *crackle, zztt* *actors are flying away down the corridor with holes in them*, etc.
-rather than a full on "HUGE BEAM SWEEPS GROUND" have many small lasers coming from the tips of the "wings" or whatever and occasionally a disruptive pulse that would cause the ground to spew up molten chunks of whatever it was (use some material rays and have some animated small molten globule MOSPs, about base gib tiny size, as well as a few animated MOSR globules.) that part would be a lot of work but OHMYGODSOSEXY. if not that, then just fire and other plasma and some misc debris. you'd need to be able to sweep the ground with it though, or it wouldnt be as cool.
-a small swarm of hellfire missles with puple and black trail smoke fired from the back of the unit up into the sky, then streaking down towards any enemies. they can just not hit the ypsilon (setwhichmonottohit())
-twin gattling guns at right angles to each other, that you can aim with the left and right controls. the ypsilon unit itself would be mostly static for this stage. as the guns fire more and more, they start to heat up (add orange glow), and once they go red hot "OVERDRIVE" comes up next to them and they start firing energy based shots rather than bullets. this stage would end with the overdrive logo blinking faster and faster and the guns exploding into a shockwave of energy, fire and debris. this one would be hard for debateable coolness.
-two pods with powerful soldiers in them eject. the soldiers last 30 seconds, after which they vaporise with a cool animation. they could have a chaingun and a cannon each, and generally be black and brutal looking.

FINAL STAGE
in a self destructive supernova of awesome, the ypsilon takes itself out, with lots of beamy energy flying out of it. would require 10 seconds of charging up, where all the shields activate and the unit itself starts overheating (again, a big red and orange glow-fest), then the beam fires downwards and causes a massive shock wave and fires, and after 3 seconds of slow motion in negative (using the palette options) the explosion happens. nom.

SUB-WEAPONS - controllable sub-entities that could get destroyed independently
-turrets on the wings to provide supporting fire
-shield units, that activate on command, drain their battery and then slowly recharge.

gah, i cant be bothered thinking of any more stuff. im just thinking it should be like an epic boss, and two of them fighting should be awesome. there could also be a mission where there is an ypsilon drifting down into a shaft with your base in it and you have to bustle about on all of the levels of this mining shaft and blow the crap out of it. if it got to the bottom, it would start its final stage and you would have to try and take out its shield nodes before it could fully charge, resulting in a premature nova of lower proportions. you would basically be trying to prevent it from nuking your brain down below, in a sort of a slow vertical scroll of increasing panic. should take 5 minutes, so that the people on trial can see the entirety of the explosion..
or maybe it should be 5m50s long so that the explosion is just about to begin when the demo runs out.

DELETE THIS POST FOR REASONS I CAN'T BE ARSED EXPLAINING. NO I CAN'T EDIT IT. YES I WILL MAKE A VALID POST.

This is basically a copy of Geti's post, because I thought that was a good template.

MAIN WEAPONS - mounted and powerful.
-Geti's ypsilon beam, with the lightning effects, only it rebounds down bunkers like an electrolaser, only it doesn't damage terrain (negative sharpness?). I like the kinetic shockwave, maybe that coud be based on the tacnuke's initial damaging air rush made of glow. You could also use lua to make it pick up and carry actors it hits, for extra impulse damage. It should be a huge beam, it should break through terrain, but it shouldn't do it too hard, like the MPAM phase-beam or something Also, make the ypsilon cannon itself disappear off the screen, as in, the cannon's only the tip of the iceberg.
-The hellfire swarm, only it homes in on the nearest enemy. They would all check eachother's targets, so they all go after different targets. Also, my swarmer bomb idea, dropping a bomb that dissolves into heat seeking missiles.
-Several materializers drop from the sides, and let loose marines, probably gunner marines. Give the beam spinup time, and in the marine's lua coding check if the cannon's spinning up. If it is, then make them get placed in craft doors in the ypsilon's main body somehow, or print a warning on the top screen, and say how long it is until the cannon fires, and give the marines a goto command to the ypsilon's doors, to be updated whenever the ypsilon moves.

FINAL STAGE
It should be a massive missile storm, where emitters on the ypsilon's sides activate, and a swarm of heat seeking or drunken missiles come out to destroy anyone who ever got close. After that, AAL forces are deployed to clean up anyone who didn't die, and the ypsilon flies out of there, to no refund, because the target painter means you never paid for it in the first place.

SUB-WEAPONS - controllable sub-entities that could get destroyed independently
-Several Amber turrets mounted on the side, and they'd be a mix of rapidfire and mega shot.
-A copy of Darlos' shield, but much more powerful. It would not only remove kinetic energy, it would reverse it, and deflect the bullets.

A mission would be good, only make it you're trying to stop someone from calling the ypsilon, and failing that, you're going to buy from their own supplier and get a ballistic MPAM to take it down. It would be fun. Tank armed with everything versus a fly with a rocket launcher.

I don't think its a wise idea to have any sort of attack for this sucker to be self destruct, or crashing it into the ground. It would kind of make the entire system unusable. For obvious reasons.

them being? if it just leaves after the final stage you still lose it, you might as well have a nice explosion for your trouble.