I don't mean to say that you should play the deck with 20/20 basics in games but to solitaire the deck while watching Netflix or something. Does it go through the first few turns more smoothly? Less smoothly? Evaluate why and then correct the specific problem from there. As a deck matures you need to bring it back to square one and re-evaluate everything in it and give the deck a refresh; sometimes our original ideas don't pan out, or recent changes lead to new lines of play and synergies.
Honestly, I think that you have too few lands in total. The Altars arent ramp pieces, but combo pieces. Mox Diamond requires a land pitch, and Mox Amber is collecting dust until your commander is out. What about Rampant Growth, Farseek, Birds of Paradise, or Search for Tomorrow? What in your deck are you willing to exile for Chrome Mox (and then why are you playing that card in your deck)? Cut out the gimmick/tapped lands and replace them with basics.
Emeria, the Sky Ruin
Flagstones of Trokair
Flooded Strand
Krosan Verge
Vesuva
Honestly, I would try gold-fishing the deck with 20 forests and 20 plains to get a benchmark, before backing that off to 15 plains and 15 forests to add some of the non-basic lands and then goldfish that again. I think the problem is that you're building a mana base that's over-complicated. One of the benefits of a two-color deck over a three to five color deck is a simplified mana base, so you really don't need to bend your back for color fixing like a 5 color deck.
What is the goal of the deck? How much mana do you need before you're in stage 2 (stage 1 is being throttled by mana, stage 2 is being throttled by card/action availability)?
Why aren't you using more of the mana dorks or ramp spells?
Do you really need City of Brass in a two-color deck?
Emeria needs far more plains.
Why is Flooded Strand in the list?
Krosan Verge is a trap, imho. You've got Mox Diamond suggesting that your turns 1-3 are important, but then why have tapped lands?
I think that you need to sit back and evaluate what your goals are with your deck and then how your mana base can supplement it. With a two-color deck you don't really need a lot of mana fixing, so you can easily cut out half of your non-basic lands. Maybe just keeping lands dropping on curve is enough for your deck and you need to focus more on card draw? What about Sylvan Library and/or Land Tax?
Re: Mirrodin Besieged, If you put it in the death star mode all of the time, then yeah, but I find that people target Sharuum graveyard with hate anyways. It also triggers at end of turn, so you can play it and nuke someone immediately.
Even if you don't have a yard when it comes into play, the other mode is still great. The only downside is that it's an enchantment.
Personally I would suggest cutting one of Open the Vaults / Roar of Reclamation and replace it with Codex Shredder. It lets you regrowth if required, and can be great for screwing with opponent's tutors. Manifold Key seems to be a direct upgrade for Voltaic Key but can also be used for kills.
I am not convinced about Marionette Master over Sculpting Steel or Disciple of the Vault. The master isnt an artifact itself so has limited interactivity with the rest of your deck. You've also minimized the clone options for the Sharuum loop. If you want to move away from that interaction then OK, but maybe its time to cut Bitter Ordeal.
Both modes of Mirrodin Besieged are great for this deck. The first is more gas in the tank, and the second outright kills people; rapidly with Time Sieve
I know this might be a little on the jank side, but has anyone looked at the stations? Blasting Station looks particularly good as it's basically a mana rock with an untap trigger; particularly with Sai.
I had been using Voidmage Prodigy since I have a handful of wizards which I can sacrifice to it, but I'll try some of the other counter critters you've listed.
I have been experimenting with Mistcaller in my deck as a meta pick, and it's been effective at stalling combos. It doesn't have quite the same 'gotcha' as Containment Priest unfortunately.
Honestly, I think that you have too few lands in total. The Altars arent ramp pieces, but combo pieces. Mox Diamond requires a land pitch, and Mox Amber is collecting dust until your commander is out. What about Rampant Growth, Farseek, Birds of Paradise, or Search for Tomorrow? What in your deck are you willing to exile for Chrome Mox (and then why are you playing that card in your deck)? Cut out the gimmick/tapped lands and replace them with basics.
Emeria, the Sky Ruin
Flagstones of Trokair
Flooded Strand
Krosan Verge
Vesuva
Why aren't you using more of the mana dorks or ramp spells?
Do you really need City of Brass in a two-color deck?
Emeria needs far more plains.
Why is Flooded Strand in the list?
Krosan Verge is a trap, imho. You've got Mox Diamond suggesting that your turns 1-3 are important, but then why have tapped lands?
I think that you need to sit back and evaluate what your goals are with your deck and then how your mana base can supplement it. With a two-color deck you don't really need a lot of mana fixing, so you can easily cut out half of your non-basic lands. Maybe just keeping lands dropping on curve is enough for your deck and you need to focus more on card draw? What about Sylvan Library and/or Land Tax?
Even if you don't have a yard when it comes into play, the other mode is still great. The only downside is that it's an enchantment.
I am not convinced about Marionette Master over Sculpting Steel or Disciple of the Vault. The master isnt an artifact itself so has limited interactivity with the rest of your deck. You've also minimized the clone options for the Sharuum loop. If you want to move away from that interaction then OK, but maybe its time to cut Bitter Ordeal.
Both modes of Mirrodin Besieged are great for this deck. The first is more gas in the tank, and the second outright kills people; rapidly with Time Sieve
Its perfect for my Urza-tron deck!