You're hitting the crack pipe if you think Death Mark has more counterplay than Death Lotus. Zhonya's and hard cc are counters to almost every champ (almost because Rengar); it's not some special weakness that Zed has above and beyond everyone else.
Zed has a 3 second delay on his detonation. Fizz's ult has a travel time and a 1.5 second delay. Kat has a 2.5 second interruptible channel in a small aoe. What you're saying is just objectively false.
It's complete and total bullshit that people repeat this nonsense about Zed's super-special unique "counterplay" and weakness to Zhonya's. The only reason Zhonya's has any special relationship to Zed is because it's essentially required to avoid dying. The Zed/Zhonya's association exists because there is no other reliable counterplay available.
You're missing the point, which is that Zed's ulti is not the problem. Too much power on his Q and W is why he's a completely broken, unbalanced laner. For example, there's no rational reason for his Q to start at 75 base damage on a 6 second cooldown with no meaningful resource investment. By comparison:
Zed's Q - 6 sec CD, 900 range, 75+37.5 from second hit
LB's Q - 6 sec CD, 700 range, 50 mana, 55+55 from second hit
Akali's Q - 6 sec CD, 600 range, 35+45, requires melee hit to detonate mark
Ahri's Q - 7 sec CD, 65 mana, 880 range, 40+40, requires 2 hits
Zyra's Q - 7 sec CD, 75 mana, 800 range, 70 after .625 sec delay
Kat's Q - 10 sec CD, 625 range, 60+15, requires melee hit to detonate mark
Now, I realize that comparisons aren't popular because you have to take an entire kit into account. Cross referencing between this selection of champs pretty much demonstrates that his Q is grossly overpowered in lane relative to other champs. Compared to assassins with the same CD, Zed's Q is aoe and does not require a second hit. Compared to Qs with similar damage, Zed's Q has a longer range, lower cost, and less delay. Compared to Kat's no-resource aoe Q, Zed's Q has a 40% shorter CD, longer range, and doesn't require a second hit. Compared to skillshots, Zed's Q has a longer range, less counterplay, and lower cost.
The problem only gets worse from there when you account for Zed's advantage via early mpen/arpen discrepancy, mages' mana tax and speed tax, other melee assassins' comparatively poor farming. All of those disparities are multiplied by Zed's W and R at level 6.
The issue with Zed is that his ulti doesn't do enough damage on its own. It has no base damage, a 1.0 AD ratio, and copies and % of the damage from his other abilities. Its functionality comes from it's "get in and get back out" mobility, but its damage depends on Zed's other abilities being far too strong.
What Riot needs to do with Zed is this:
Q: Lower base damage to 55, scaling cooldown from 9-5 sec, reduce scaling energy cost to 70-50
W: The shadow functions like Pix casting Glitterlance. It's an extra chance to hit in a larger area/range, but enemies can only be damaged by one ability. Zed's E already works this way. Cooldown reduced by X when the shadow damages a champion.
E: Lower base damage to 45
R: Cooldown reduced to 100/80/60. Add high base damage on application (like 200/400/600), Zed and shadows can damage targets with the same abilities and deal 75% of the ability damage on the second hit for 10 seconds. (Numbers subject to tuning, obvs)
Basically what this does is bring Zed's laning within the limits imposed on every other mid laner. He's less oppressive in lane but has a stronger assassination combo if well-executed. It's more counterplay overall and gives Zed a longer window to play around a Zhonya's on his ult proc with less dependence on the proc itself (because of the initial damage). Lastly, lower CDs and energy costs late game and some sustained damage options on his ult would help shift some early game dominance to mid/late game relevance.