3-2 Houndoom (1 prime, 1 non)
1 Rescue Energy
5 Special Darkness
1 Flowershop Lady
1 Lost Remover
1 Pokemon Communication
1 Professor Oak's New Theory
1 Professor Elm's Training Method
Deck Total = 53 (Need 7 more cards for a full 60 card deck)
You've got some great pokemon in the deck, but you have way too many different pokemon that don't always work together. I immediately noticed that you have somewhat of a disruption deck going on. Weaville and non prime houndoom can reduce your opponents hand size by forcing them to discard cards from their hand. The houndoom prime can burn from the bench, which can force your opponent to retreat to prevent burn damage. I'm not sure which honchkrow you have, but running a couple of the one with shadow binde would be ideal If you can burn them and use honchkrows shadow bind, they can't retreat out of the burn. The other honchkrow is more powerful though, being able to snipe for 50, so perhaps including one of those would be a good idea too.
I like xatu's attacks, so I would keep it in, but I don't think this deck is going to be fast enough to run the stage 2 nidoqueen. I would also drop the spritomb and sableye. I like grumpigs second attack, so it might have a spot in this deck. I like the tyrogue in order to KO your opponents baby pokemon and possibly stall, but you will also need a starter pokemon yourself, like a cleffa or manaphy.
You need to get a few more copies of the pokemon that you decide to focus on. If you have 3 sableye, then you should run 3 weaville. Running only one copy of a stage 1 pokemon is tricky, because if it get's KO'd quickly, you may not have a backup plan. I would focus on increasing the weaville and houndoom lines, maybe running 2-2 honchkrow (one of each), and 2-2 of grumpig and xatu. Some playtesting will show you which of these pokemon you really like to attack with, and once you find that out, you may want to continue to increase the lines of those and drop others that you don't use as much.
You could also consider dropping a pokemon line and adding in slowking who's power allows you to look at the top 3 cards of your opponents deck and rearrange them. This could be another way to slow down your opponent!
You can only have 4 special energy per deck, so you'll need to reduce the special dark to 4. Since you run more dark pokemon than psychic, I would also increase the regular dark to 5. I would drop the rescue energy simply because with only one in the deck, you may not be able to draw into it to use it when you want.
This is the section that needs the most work. 8 cards to try and get the pokemon/energy out that you need is not going to be enough. So we start by adding in cards to search for basic pokemon like pokemon collector or dual ball. Elm is fine for searching out higher stages, but I prefer increasing the communication so you can just swap whatever you have in your hand for whatever you need. You'll need more hand refreshers like professor oaks new theory and copycat(you can have a max of 4 of a card per deck), a juniper and possibly adding in some cheren to be able to draw more. For recovery, you have the flower shop to get cards back from the discard pile, but you'll need twins in case you're behind. Junk arms will allow you to reuse your trainers and pokemon catcher will let you drag up your opponents benched pokemon to either stall or to get easy KO's. You shouldn't need the fisherman with the flower shop since you shouldn't be losing a lot of energy.
Since you have pokemon that disrupt, the lost remover could be a good addition, but I would just keep one in the deck. I would increase your number of switch because of other decks using pokemon catcher to bring up your benched pokemon. Since you run cards that force your opponent to discard from their hand, I would also add in 4 team rockets trickery just to force them to discard more. You could also add judge in to reduce their hand size before you attack with houndoom to force them to discard, but this might take a bit of practice to play the right way (it's easy to judge yourself into a bad hand when you're bench isn't prepared).
By tripling your trainer/supporter line and reducing your pokemon line, you should have an easier time getting what you want when you need it. While your deck doesn't attack for a high amount of damage, it has quite a bit of disruption to slow downI hope my suggestions help!