3-2-3 Samurott (2 w/ability)
pokemon total = 24
3 team rockets trickery
2 flower shop lady
2 engineers adjustment
2 poke collector
3 energy retrieval
2 rare candy
3 poke com.
2 energy search
trainer/supporter total = 19
energy total = 14
Deck Total = 57
The first problem with this deck is that you need 60 total cards. There's plenty of trainers and supporters that can be added though, so it's good that we have 3 extra spaces to work with at the moment.
Cleffa is used to help get the deck going by using its attack 'eeeeek' to shuffle in and draw 6. While it puts cleffa to sleep, if it can stay asleep, its pokebody says that it cant be hurt. Since you're already running babies, I would include 1 tyrogue to possibly be able to knock out your opponents cleffas. The dodrio allows you to retreat without having to pay 2 energy cards for the retreat cost. This is perfect for this deck since all the pokemon have a 2 or less retreat cost, therefore with dodrio on the bench, they can essentially act as if they all have free retreat. The first pokemon you're probably going to be attacking with is likely going to be reshiram since its first attack only needs 1 double colorless energy. Reshiram also acts as a great counter to decks that attack with kingdra prime since when a fire pokemon is in play, it reduces the base damage of kingdra from 60 to 20. But since you have to discard 2 fire energy, you might want to reduce the number that you run to 1.
The samurott line is your strongest line of pokemon and the line that will take the most time to get up and going. Ability samurott can reduce damage done to it by 20 and can also hit more for each water energy attached to it. The non ability samurott can snipe with the attack pike (which also hits the active), The second attack is also strong, but I would primarily use this as a sniper card to spread some damage around. The cincinno in this deck is also incredibly strong, doing 100 for only a double colorless as long as the bench is full. Zoroark is a great counter to just about everything since it can copy your opponents attacks. Except for the addition of a tyrogue and the withdrawal of a reshiram, I wouldn't change the pokemon lines.
All of your pokemon can make use of double colorless energy, so I would increase the number to 4. I doubt that you'll be using reshirams attack very much since you have to discard, so it should be safe reducing the amount of fire energy to 3 or 4. You could possibly reduce the water energy by 1 or 2 as well and still be able to draw into them very easily with the right trainers and supporters.
You should increase your basic searching cards to at least 3 if not 4 (pokemon collector is preferred but dual ball is a good subsitution). The 3 pokemon communication is a good number for being able to swap the pokemon you don't need at the moment for the ones that you do need. 2 rare candy is the right number for trying to evolve those samurott as fast as possible although if you're finding that you need more space in the deck, since you run 2 dewotts, you'll probably be safe going down to 1 rare candy. You can always reuse it with the addition of 3-4 junk arms (as well as any other trainer that you run). I would suggest adding in 1 twins since yanmega decks are extremely fast and they'll likely be getting the first prize. Twins will help you get back in the game.
Since I recommend focusing less on reshirams second attack that makes you discard energy, I would reduce your recovery line to 1 flower shop and 1 energy retrieval. Those should be more than enough since you have quite a few attackers in this deck. I think you need some cards to refresh your overall hand like professor oaks new theory, copycat and juniper. I wouldn't add more than 1 juniper, but would add 4 oaks new theory and possibly a couple of copycat. To make room for them I think you can easily take out the engineer and rockets trickery. If you were going to keep either one of them in, I would leave in engineer since you can always use energy retrieval/junk arm to be able to get the energy back. With the hand refreshers and around 14 energy, you shouldn't have any problems drawing into energy, so I think you could drop the energy search. If you have any room left, I would add in 2 pokemon catcher to bring up pokemon from your opponents bench for easy knock outs, or even stallers while you snipe with samurott.
Your lines of pokemon are pretty good already and I think with some tweaks to the trainers/supporters and energy, you should be able to really get this deck going. I was running a deck very similar to it earlier in the year and it has quite a bit of potential, especially with the addition of pokemon catcher.