Pulling from EDHREC to see what cards are popular with Marchesa, I see several that might draw your attention, and I’ll go over why I’m not running many of the most popular options.
Flayer of the Hatebound/Stalking Vengeance/Warstorm Surge
I actually used to run Flayer back in the early days, along with Stalking Vengeance, but they’re both just so incredibly expensive. By that stage of the game their effects aren’t even that important either. For 6-8 mana there’s a lot of better things you can be doing. If you run them see how many games you go where they just sit in your hand as you say “hmm i’ll play them next turn maybe”
Herald of Secret Streams
Making most or all of our creatures unblockable seems great, we can get in for a ton of damage or even knock someone out. But truth be told it’s not that important. If you attack and they do block you’re coming out ahead on the trade 9/10 times and so there’s not really much downside there, you’ll have a clear board the next turn probably. And we’re practically immune to board wipes, so we don’t have to worry about that the board getting too full to attack through either. I’d rather run Damnation in this slot given the choice since it’ll be a lot more effective at solving this problem.
Dack's Duplicate
I’d opt for Phyrexian Metamorph as it can copy creatures or artifacts, and potentially costs 1 less mana. The haste and extra instance of dethrone aren’t that important compared to the flexibility of being able to copy artifacts and creatures. i opted for Spark Double as a clone effect though.
River Kelpie
I recommend Grim Haruspex instead. It’s 2 mana less and does essentially the same exact thing for our purposes not to mention it's less color pips, has morph if needed, and is also a wizard.
Grave Betrayal
When it hits it’s pretty cool, but for 7 mana it’s not going to hit often. I spent far too many games with this just clogging up my hand and haven’t missed it once since I cut it.
Sidisi, Undead Vizier
The tutor package I’m running seems to work well enough that I haven’t bothered with her.
Captivating Crew/Mark of Mutiny/Threaten/Zealous Conscripts/Act of Treason/etc etc
Stealing things with these effects is a popular strategy people play with marchesa, but I’m not going that route, so these cards have little place in this version of the deck.
Grimgin, Corpse-born
He’s a sac outlet that makes his own +1 Counters, but if you don’t have a creature to sacrifice he is useless and also ultimately he’s a 5/5 beater with no evasion. I’d rather run a cheaper sac outlet or a better beater.
Thraximundar
He’s very expensive at CMC7. while he’s a strong threat for the late game I’ve been tuning my deck’s average CMC lower, so cards in the 7 drop slot have been making their migration. He generally is impactful as soon as you play him since he has haste and a built in way to get +1 counters, but i think his place is in a more battle cruiser type meta.
Exava, Rakdos Bloodwitch
This card does nothing. I have no idea why people run it. All your creatures come into play at EoT from Marchesa’s ability, so that means if you sacrifice them on your opponent’s turn they can still attack on your turn. The creature’s we have available that come in with +1 counters by default aren’t really that important to attack with in the first place. do you just reallllly need to swing in with that arcbound worker right away on T5? She’s a 4/4 for 4 mana with no evasion in two colors with an irrelevant ability. I don’t see any reason to run her.
Puppeteer Clique
At 5 mana this guy is relatively expensive and honestly my opponents usually don’t have anything better for my game plan than I do, so there’s not usually much need for the ability. That said, you might have a use for him in the right meta, but i generally avoid him.
Burnished Hart
I feel like 3 mana per use is a bit much for this and there’s only so many basics in the deck. I’d much rather run Solemn Simulacrum
Falkenrath Aristocrat
it isn't a bad card, but Yahenni, Undying Partisan is better. Why not both? Gotta make room for cards somewhere.
Butcher of Malakir
What have I been telling you about 7 drops?
Treasonous Ogre
We have better ways to control our life total than this and we’re pretty light on red cards, so the mana isn’t really needed either.
Necropolis Regent
many of our creatures make +1 counters out of combat, so the ability isn’t needed that much, and at 6 mana it’s even less worth it.
Triskellion/Walking Ballista
I just don’t want to run the combo, but you totally can.
Runescarred Demon
What are you trying to do? Run a mono 7 drop deck here? How many times do we have to teach you this lesson old man? Running Sidisi or most other low cost tutors is the better option I think.
Marchesa's Smuggler
See Herald of Secret Streams
Noxious Gearhulk
I’m cautious about including too much lifegain in the deck, and at 6 mana he’s a bit tough to play as he’s getting to the top of our curve and is essentially just a removal spell anyway. I prefer Merciless Executioner type effects for looping removal.
Sheoldred, the Whispering One
We’re not really going to have very many creatures in our graveyard to make use of, and she paints a huge target on your head when you play her for .. 7 mana.
Noosegraf Mob
Not a bad way to get bodies on the floor, but you’ve got to have a sac outlet around and you’re only making 2/2’s with your 6 mana time sink. There are better ways to make tokens in my opinion.
Chasm Skulker
Actually this is not a bad option. it's definitely something you could consider. So far I've found other options like Desecrated Tomb provides a larger number of tokens to the board over the course of a game though, and flying is usually more relevant than islandwalk.
Vigean Graftmage and other Graft creatures
By and large they all have pretty useless abilities so I’d skip almost all of them.
Reef Wurm
It always took me way too much effort to get this thing moving. It’s cool when it works and you’re pumping out a 9/9 every turn, but it just didn’t happen enough for my liking.
Brainstorm
Personally I don’t rate it very highly in EDH since you just don’t really have high enough fetch land / shuffle effect density to make great use of it like you do in Legacy. Cards like Ponder and Preordain are better here.
Living Death/Animate Dead/Reanimate/Necromancy/etc
We’re not running a reanimator deck, we’re running a recursion deck. Our creatures typically aren’t in the yard more than a phase or two, so these effects aren’t very useful. A single Phyrexian Reclamation should be enough for our needs. Living Death has some utility as a pseudo board wipe though.
Attrition
Black is a very popular color in EDH, so I avoid Doom Blade type effects.
Sneak Attack
Honestly I prefer Shifting Shadows for cheating creatures out. Shadows guarantees you get something every turn, whereas Sneak Attack requires something in hand. Not to mention that by and large our creatures aren’t terribly expensive to play, so I think finding them in the deck is a bit more important than merely cheating them out.
if you are looking for a cheaper way to cheat things out then Scroll of Fate is a good option that can even let you ramp lands.
Oblivion Stone
It's not actually any great savings on mana compared to Unstable Obelisk, All is Dust, Perilous Vault or Scour from Existence since it still costs 8 mana to use it, and if you want to save anything it costs even more, as well as placing a large target on your head.
Midnight Reaper
For me Grim Haruspex synergizes better, and personally I'm not a fan of the life loss on reaper being mandatory when the same effect is free on GH. There are plenty of life total manipulating effects in the deck as it is, but you could definitely run this card if you want to. Especially if a card like Necropotence or Rhystic Study is out of budget.
Blood Tracker
I felt that Toothy, Imaginary Friend would be a better option since it doesn't require any upkeep, but i've elected not to run either at this point as Impaler Shrike has been performing a bit better for me lately.
Grenzo, Dungeon Warden & Timestream Navigator this is a pointless 3 card do nothing win more combo that should never be run in this deck. the time and effort involved in piecing this jank together in any given game is not worth it. these two cards have no other synergy with the deck in any way and should absolutely not be given a second thought. if you're going to run a combo you may as well run a better one considering it'll probably require less effort for most of them.