Ok, so you have a 1-0-1 Kingdra that you can't get back. Big deal. use your other 3 Kingdras.
The main flaw I see with the lost zone is that the pokemon have the inability to score OHKOs. Giratina IFDS has a damage output of 50 for 3? Good job, you can OHKO a Ralts. By the time you have three energies on Giratina, I will be keeping all my pokemon that are in range of being KO'd benched. And not to mention Tyranitar = OHKO for two energy. Machamp = OHKO for one energy. Magmortar = OHKO with five energy (not that hard if you use Leafeon Lv.X).
Giratina Lv.X is better than normal Giratina IFDS (obviously, its a Lv.X). But still, with the same principals as Giratina, by the time you have 4 Energy on it, I will have prepared my self for the 30 Snipe. It does have 30 more HP which saves it's tail in the long run from Tyranitar easy KO's, but Machamp still OHKOs you.
Dialga G Lv.X is a pokemon that I could see causing some disruption. It can shut down PokeBodies which can hurt Tyranitar. It's ability to put energies in the lost zone is dangerous in the fact that you can't get them back. But how many heads can you flip? And if I see the Dialga, I'll know to spread out my energies just incase something terrible were to happen with you coin flips. It does have a good damage out put of 80, but unfortuanatly a lot of Stage 1 pokemon now have 90 HP instead of the usuall 80, meaning you lose the OHKO factor. PP and Buck can always help though. Dialga G (non Lv.X) could cause some disruption with Pierce ([m][c] 10 no Trainers or Stadiums next turn) but in the end, Dialga just seems slower than Giratina, and is weak to fire. By the time these cards are out, we'll have Shaymin Lv.X, and all the uber Grass pokemon in SF, meaning that Kingdra and other water decks will not be able to keep up. These two factors plus people exmerimenting with Heatran Lv.X means Fire will be more popular. Magmortar gets the OHKO for only 3 Energy (unless you have Metal), and again, Machamp gets the OHKO no matter what.
Palkia G Lv.X is the only card that makes me a little nervous. The fact that it doesn't have to even attack to put pokemon into the Lost Zone can keep people on their toes. The sad thing is though, is that once I see the Palkia Lv.X, I won't play any more benched pokemon. But the thing that makes it a card that you can play around is the fact that each player gets to choose which pokemon get sent to the lost zone. Another sad thing is, is that if you use a starter in your deck (and this format, people are finding that starters are going to be needed more and more) and it got stuck on the bench from a Warp Point/Retreat, it would be my first choice to Send to the Lost Zone. If I still have to choose a pokemon, any "bench sitter" tech (such as Azelf or Uxie who activate only when you play them down and then you never use them the rest of the game) would also be candidates for being Lost Zoned. It's attack isn't too much to fear, since I doubt it will ever attack. If it ever becomes active, Machamp OHKO's it, along with Raichu Lv.X (that is, if it survives untill we get GC).
Overall, I don't really think that the Lost Zone is something to be scared of. The pokemon require too high of an energy cost to pull off a quick unexpected KO into the Lost Zone. Luxray will always linger in this format, there is nothing we can do to stop it as long as Lv.X's are being played, and if you use one of these pokemon, you will get hurt, and badly. They all have a common theme of suffering from Machamp, who I can almost guarantee will not be forgotten when we get GC. They all have weaknesses that really hurt and cause them to be KO'd easier. They all lack the damage out put (with perhaps the exception of Giratina Lv.X) to score OHKO's on almost all Stage 2 Pokemon, and some of the Stage 1 Pokemon that are in the Metagame. They are all easy to play around, and not very easy to set up. All in all, Palkia Lv.X is really the only one that you have to worry about, and still, it can be played around. The fact that they have to be active to get the Lv.X also can be a pain, but Level Max may be a way to work around this issue.
Also, just to point out, that all though the Lost Zone may exist in two Japanese Sets, we will probably not get Giratina in our SF, but get it in time with the Movie, meaning that we will only have Lost Zone pokemon in our GC.