It can be frustrating. There are times when an enemy definitely should not be considered off the ground but appears to be anyway. Other than applying a -fly power, my usual solution is to scan for another target that appears grounded and target it for roots. Truth be told, I use roots so early and so often in a fight that it hasn't been much of an issue for me.
Quick question...while ghosts can be difficult to immobilize, they generally aren't difficult to hold unless they've applied significant tohit debuffs on you. This suggests to me that you aren't using seeds of confusion to start the fight. Is that correct?
Dark Armor/Stone Melee Tank Guide [I12]
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It can be frustrating. There are times when an enemy definitely should not be considered off the ground but appears to be anyway. Other than applying a -fly power, my usual solution is to scan for another target that appears grounded and target it for roots. Truth be told, I use roots so early and so often in a fight that it hasn't been much of an issue for me.
Quick question...while ghosts can be difficult to immobilize, they generally aren't difficult to hold unless they've applied significant tohit debuffs on you. This suggests to me that you aren't using seeds of confusion to start the fight. Is that correct?
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No, I do use seeds of confusion, roots, rad infection (rad 2ndary) entangle / strangler.
The problem is, even when confused, CoT ghost will become invisible and take off. Very much like the Tsoo Spirits do. If I have more than one running, when they come back, they're mad as all get out. If seeds or strangler isn't ready yet, it takes one roots and one entangle to get one immob. I just hope that I can get a good hit on the other. I have one accuracy in roots, strangler, and entangle. I have 2 accuracy in seeds. I can usually recover the situation, but it still makes it harder when they're tagged in flight even when they're not looking like it.
Demonfest - 50 - Demon / Thermal Mastermind
Covered Shadow - 50 - Dark Melee / Shield Scrapper
Ah. Yeah it's annoying when they take off. Slotting strangler was a definite priority for me, and I was usually able to hold the ghosts before they decide to do so.
May want to add more accuracy in roots. Like many AoE control powers it has a lower base accuracy than 1. Strangler and entangle, on the other hand, start with a higher accuracy. Interestingly enough, seeds actually has a base accuracy of 1, though I could see slotting it heavily for accuracy anyway given its importance.
Dark Armor/Stone Melee Tank Guide [I12]
OK with /Rad, you will want Radiation Infection with some defense debuff in it, then Nemesis Staff them before you apply the hold. That will knock them to the ground. Then you can hold them and root them. If you hold them in the air, then you have no way to knock down; at that point you're screwed.
Or you can find something nearby who is on the ground ( thorncaster or something ) and roots them, the aoe will catch the spirit. If you have Hasten, AM, and RI the Nemesis Staff approach will be your best bet - giving you good recharge for the staff, and good defense debuff to hit with.
Eventually Carrion Creepers will be knocking them down for you so you won't have to worry much about it.
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OK with /Rad, you will want Radiation Infection with some defense debuff in it, then Nemesis Staff them before you apply the hold. That will knock them to the ground. Then you can hold them and root them. If you hold them in the air, then you have no way to knock down; at that point you're screwed.
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Oh Yeah, I found out the hard way on that. I kicked myself for that one.
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Or you can find something nearby who is on the ground ( thorncaster or something ) and roots them, the aoe will catch the spirit. If you have Hasten, AM, and RI the Nemesis Staff approach will be your best bet - giving you good recharge for the staff, and good defense debuff to hit with.
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I have both hasten and AM. It does help alot with the recharge rate. 
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Eventually Carrion Creepers will be knocking them down for you so you won't have to worry much about it.
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As soon as they become available at 26, I have them planned for. That's going to be party time for me!!! 
Thanks for the help ! I'll work more with Nemesis Staff on those bad boys. I know I'll be facing them for quite a few more levels.
Demonfest - 50 - Demon / Thermal Mastermind
Covered Shadow - 50 - Dark Melee / Shield Scrapper
If Flight is your travel power of choice, then taking and using Air Superiority will also give you the -fly power that you are lacking.
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-I do not feel obliged to believe that the same God who has endowed us with sense, reason, and intellect has intended us to forgo their use. - Galileo Galilei
-When injustice becomes law, resistance becomes duty. - Thomas Jefferson
QR
This is one of those situations in which Snow Storm in the /Storm set is very handy for its -fly.
If you don't have a -fly power available, as has been noted, if you can hit a baddie on the ground with Roots, very often the AoE will "splash" onto nearby fliers. I have noted this when trying to keep Roots on baddies getting buzzed down by Tornado. Sometimes I am just a hair late and baddies get flung before I can fire Roots off. I have seen Roots hit someone with the "splash" that was being held in the air in a corner by the Tornado, whereas it would "Target in Air" if fired at him directly.
I suppose it "logically" makes sense that the plants have to be able to grow up out of the ground in order to grab the baddies, and it adds that element of challenge to playing Plant. I do like it that not every Controller set is exactly the same with just different animations.
"How do you know you are on the side of good?" a Paragon citizen asked him. "How can we even know what is 'good'?"
"The Most High has spoken, even with His own blood," Melancton replied. "Surely we know."
I've been using these new tricks and it seems to be getting easier. I have been using my Air Superiority for the beat down, but I've also been using the Nemesis Staff to a greater success. The reduced defense in Rad Inf is making a big difference. Seeds is coming back up faster with an additional recharge in it too, so even if they come running back, I can get them to start hitting a different target or just sit there while I finish them off.
Oh, speaking of Seeds. I'm starting to hit the Raiders. I'm letting the engineers make their shield drones before casting confuse. Yeah!!! I get bubbles. This is so awsome!
Thanks again All !
Demonfest - 50 - Demon / Thermal Mastermind
Covered Shadow - 50 - Dark Melee / Shield Scrapper
Creepers also has -fly, and the Fly Trap I believe has a -fly as well.
I am becoming more frustrated with Entangle and Roots and how they apply to fliers (or don't, in this case). It tells me that the target is in flight even though they are showing very close to the ground. It only seems to get worse as I fight higher levels now. Circle of Thorns Ghost are becoming the worse offenders. Im using my Air Superiority to try to beat them down, but theyre so hard to hold and immobilize as it is. Any tricks out there that I can use? I have vet powers Sands of Mu, Black Wand and Nemesis Staff, but the recharge is slow and the accuracy is 50 / 50. I just keep chipping away at them as they run off, life steal and continue to decrease my accuracy with every hit.
Demonfest - 50 - Demon / Thermal Mastermind
Covered Shadow - 50 - Dark Melee / Shield Scrapper