We still have a problem with the only one card thing. We also have some less than desirable trainers. Those are the main problems with the deck. Let's see if we can't fix this.
You have that mix of bench damage and Rain Dance. Rain Dance is an old style of deck that I used a fair amount back when I played the game, so I feel pretty experienced in it. I know that the deck has to be built around Blastoise, and that it doesn't work quite as well without massive card draw and more of a Water focus. As such, I would suggest removing the Blastoise line. Since Keldeo is really designed for use in Rain Dance, we can remove it as well. Raikou EX is kinda awful, so we'll remove it. And then we can remove Mewtwo EX because it really has no point here. Black Kyurem is average, but it can be replaced by better basics. Milotic is a very nice card, but Feebas makes the line too vulnerable for my liking. We could keep it, but I would suggest removing it to make room for more cards. Vaporeon we can also remove, as it isn't all that great. As much as I'm loathe to, we should also remove Kingdra. It's a great card and has bench damaging. Thing is, it's a stage 2 and it is a better fit in a discard style deck. Its removal can pave the way to some better basics and Stage 1s.
Let's get some Basics in there. One card is always a great idea for a bench damage deck, and that card is Kyurem http://serebii.net/card/noblevictories/034.shtml
High HP, power when it gets to low HP, and bench damaging, this card is a must for any bench damage deck, so we'll add three. We'll then support it with four Emolga http://serebii.net/card/dragonsexalted/045.shtml whose Basic getting powers, one for 20 attack, lack of retreat cost, and Fighting resistance all make it a great card in the early game. EX wise, let's add a couple of Kyogre EX http://serebii.net/card/darkexplorers/026.shtml which have nice bench damaging and high HP. Onto the evolution lines. Let's bulk up that Electivire line a tiny bit by adding another Electabuzz and another Electivire. Then, let's add two Sharpedo http://serebii.net/card/plasmastorm/033.shtml and two Carvanha http://serebii.net/card/plasmastorm/032.shtml
Energy wise, let's drop it down to 13 energy. Four of them will be Blend Energy http://serebii.net/card/dragonsexalted/118.shtml and then we can have six Water energy and three Electric energy.
This leaves us with room for 30 trainers. First the Trainers you have. Skyla is a great card. I prefer using Juniper over N, but we'll keep N as a drawer because it is safer to use. Cheren is great drawing. Shadow Triad has no place in the deck due to a lack of Plasma cards (Ghetsis is something that I'm not too sure how useful it would be. I was a huge fan of Lass and Rocket's Sneak attack back in the day, but due to providing the opponent with card draw, Ghetsis isn't even close to the caliber of these cards. I don't like it and think there are better Trainers to use.) Pokemon Communication is great. Great Ball is outclassed in terms of card search. Hypnotoxic Laser just sucks. Superior Energy Retrieval doesn't have as much use in this era of SERlessness, especially when the deck doesn't use lots of discard. Godd card, just not a good fit for this deck. Town Map has limited use and should be replaced with better Trainers. Plus Power is decent, but it is limited also. We can remove it. We have cards like Emolga, Sharpedo, and Kyogre EX, so Switch isn't really needed. Energy Retrieval is bad now that Superior is out. And Energy Retrieval doesn't fit in with the deck. We will be adding some energy gain though. Energy Search is nowhere near as good as other Trainers, especially ones that draw cards. Rocky Helmet works great with Sharpedo. Float Stone is not needed. Giant Cape is pretty blah.
So what Trainers should you have? Four Pokemon Communication, four Pokemon Catcher http://serebii.net/card/emergingpowers/095.shtml , four N, four Cheren, two Super Rod http://serebii.net/card/noblevictories/095.shtml , three Rocky Helmet, four Skyla, one Computer Search http://serebii.net/card/boundariescrossed/137.shtml , and four Crush Hammer http://serebii.net/card/emergingpowers/092.shtml
Catcher is pretty much the best Trainer in the game. The manipulation of the opponent's bench fits in perfectly with this deck. Include four in every deck you use. Super Rod gets back Pokemon and Energy, making it an easier fit into a deck than Retrieval. Computer Search is a great Ace Trainer, and should usually be the one you use in your deck. Card search is very important. Crush Hammer are just some filler. Discarding energy can be nice.
So the deck would look like:
x2 Kyogre EX
x4 Pokemon Communication
x4 Pokemon Catcher
x4 Crush Hammer
x3 Rocky Helmet
x2 Super Rod
x1 Computer Search
x4 Blend Energy WLFM
When the set Megalo Cannon is released in the US, you can replace some Trainers. Replace one Rocky Helmet and all four Crush Hammers for three Silver Mirror and two Iris.
Edit: Replace the four N I had previously suggested with four Ghetsis. I was going off the old Japanese translation for the card, which is actually incorrect. Ghetsis is in fact not awful but actually an incredible trainer combination of Lass and card draw.