LostGar was an ok deck, but was mainly just popular because of hype.
First off, the MewGar version of this deck is no longer viable because all a deck has to do is set up a Donphan or Cobalion or Zekrom to knock out a Mew each and every turn giving MewGar nothing to seeker up and Lost Zone.
Lostgar isn't popular this format because of decks that don't use many Pokémon, and big attackers. Despite Gengar having the "magic" HP number, a numerous number of Pokémon can ko it, such as Magnezone, a very popular card. Even back at Regionals last year when I was playing Magnezone, it just kept consistently discarding my Pokémon with Regirock's power, which can be replaced by Junk Arm.
The other reason Lostgar isn't very popular is because of cards such as Junk Arm, Sage's Training, and Professor Juniper. All three discard cards, and there are different discarding related strategies behind all 3. With Junk Arm, you can use Junk Arm after using a Pokémon Collector to get rid of basics, or just Junk Arm away evolutions after they lost zone the basic. Sage is random what you draw, but against LostGar you can just discard all the basics, so your not as stressed to decide what to choose. Juniper can be used if you have a relatively low hand but one or 2 Pokémon. There is not very much you can do to support Juniper by giving it more Pokémon to discard, but every discarded Pokémon hurts LostGar.
A supporting factor for LostGar is no more fossils. Fossils were a big problem for LostGar, because that one card tech destroyed the deck. The new fossil mechanic is a supporting factor for why LostGar should be popular, but there are still too many problems with LostGar for it to work.
Basic oriented decks such as ZPST are now popular, so that means a lot less Pokémon that could be lost zoned. Zekrom also sets up way before speed LostGar does, giving more chances to take knockouts and discard Pokémon before LostGar sets up. Decks like Coke also discard Pokémon as part of setting up, and can do a lot of damage while locking attacking.
There are also new favorable matchups for LostGar now too however such as The Truth and ChandyPlume. These could cause LostGar to see a bump in play because of the large number of Pokémon played in it. Durant is another extremely favorable matchup for LostGar. LostGar easily beats Durant because once Durants are lost zoned, there are no way to get the Durants back. This means each turn when LostGar uses Seeker or attacks, the next turn Durant can only discard one less card. Though Durants only using 5 Pokémon on average may seem a problem, it is also easy to make Durant run out of Pokémon by using your Seeker's, and then use the attack to knock out the final Durant.
Lastly LostGar is hard to play as DNA has stated. I played it for a while, and I didn't have any problems with playing it but eventually some hard decisions may have to be made.