RisenDeep

While playing with counters just invest into some Astral Cornucopia and Everflowing Chalice and some Coretapper

As most Merfolk are also Wizards, you could play Patron Wizard as well as counter enabling and it showed that Nissa, Steward of Elements is a good Aether Vial replacement

Like her, was funny to see my opponent getting nervous when she enetered the board :D

As a long term Proteus Staff enthusiast I would remove Silvan Scrying and instead add a lot more land support so your intention should be to get Proteus Staff/Polymorph out as early as possible. Explore, Farseek and Search for Tomorrow should however stable your mana base in combination with Utopia Sprawl. In a more expensive version, I would play Lotus Bloom instead but ok.

Khalni Garden is a good idea for getting a token, I did it using Mutavault/Inkmoth Nexus in my early version

What about Isochron Scepter to copy spells like Early Frost?

Do you know about the Hinder/Tunel Vision combo?

It only works in EDH matches because each card is unique you may send a card under your opponents library with Hinder and then Tunnel Vision name it to let him discard his full deck at once

Lead the Stampede or Collected Company could be great extensions to this deck for getting more elves out. One additional power drop is Oran-Rief, the Vastwood because it helps casting your Joraga Warcaller for 2 instead of 3 mana and still have a counter on it.

I would completely remove Comet Storm for Banefire. It has the advantage to be uncounter/unpreventable so your final strike is safe. Otherwise Comet Storm is an easy counter target for at least Spell Pierce

Cut the Sovereign and instead increase Master of Waves and add Phantasmal Image

What I think of is a bit more Steampunk related thinking on the Dishornored game series, especially the mechanic soldiers, you might think of Walking Balista and other construct soldiers like Soldier Replica

There are so much guys, why not go for Collected Company?

Merfolk in modern budget is playable but it needs some structure to get success. It turned out for me that splashing to White makes the deck more competitive

http://www.mtgvault.com/risendeep/decks/merfolk-bdg/

Dont play Triton Shorestalker, play Cursecatcher instead as 1-Mana card and/or use something with better performance like Inkfathom Infiltrator or River Sneak that both have advantages, at least in power.

Never have seen Smuggler's Copter yet in a Merfolk tribal deck for reasons like bad late game performance, Flying vs. Islandwalk and so on. You will have enougth cards in hand so dont worry about that.

The 2 drop Mana Leak seems ... well ... neat, it might be a dead counter card when played late game and you will mostly not use it/ have it in earlier turns so either decide for something more reliable like Remand or put a couple more of them into your deck/replace them by potentially Rune Snag because it raises worth in late game.

While you wrote it is Modern but did not tag it as Budget; I'm also missing an essential key card Aether Vial in this deck and/or some Chalice of the Void

An interesting approach I will investigate a little further; +1

What I'm missing in this deck are three important cards that support this kind of deck very much:

- True-Name Nemesis, a must have for Merfolk EDH, however the card speaks for itself

- Grand Architect, not only powers your blue creatures but also heavily increases your artifact output while have your blue creatures produce (2) to play artifact spells and abilities

- Parton Wizard, because a good set of your creatures are also Wizards, this card enables you to counter spells by just tapping your merfolk creatures for it. Due to Merrow Commerce you will have untapped Wizards each of your opponents turns so use them

Then there are a LOT of other potential cards you could use for especially EDH, for example Empress Galina, a admitted mana intensive card but for its ability worth the price. Ever wanted to take control of your opponents commander and legendaries, Empress Galina is your girl (or fish or whatever... ). Kira, Great Glass Spinner as an exchange option for Tada Adel when playing against hate heavy decks. Dakra Mystic as draw/hate card could reject your opponent by drawing important cards or give you a card advantage. Sea Scryer for some extra mana and an additional hitter in late game. Stoneforge Masterwork and Sword of the Animist are great equipments to wera for especially Thada Adel, while Stoneforge Masterwork powers a single Merfolk you will get an additional land each turn with Sword of the Animist.

Just to name a few examples

And one single Blood Moon beads them all :p

There are still outiseders with a little bit of imagination beyond the masses that copy tourney decks ;)

Not entirely unless you decide to go for Metallic Mimic

I run this version
http://www.mtgvault.com/risendeep/decks/merfolk-11/

Steel of the Goodhead is absolutely playable as a one or two drop

You are welcome. So Cavern of Souls are expensive too so why not trade them for Aether Vial ;)

What I play in my standard list is also Rishkar, Peema Renegade to also have a mana benefit from all the counters (and he brings counters when playing too) but it isnt a merfolk too so may not trigger Deeproot Waters. However, the mana benefit may make the game