Vel's ult just feels bad now no matter how you use it.
But before I get into that, I want to talk about what I do like about the rework. The first is the shifting of his abilities to maxing Q first over W. This creates much more interesting gameplay and forces you to interact with your opponent more often which is beneficial for both players. I also like the removal of the Q indicator for Vel's opponents; frankly, it was ridiculous that they ever got to see it in the first place. I also really like that his passive now scales with AP at the expense of AP scaling on his W and E: this makes landing your passive more important and gives his opponents more counterplay against him while making good play on his part more rewarding than before.
However, I greatly dislike how the ult was changed for 1 very simple reason. With the changes, Vel's ult now has 2 different and distinct uses, neither of which feels satisfying compared to before. The first is to simply use it how it was used before, mainly as long ranged follow up to an allied initiation of counter-engage to an enemy initiation. Your goal is to hit as many enemies as possible and inflict as much AOE carnage as possible. However, this is almost always worse to do than it was before since your ult no longer grants passive stacks; that big burst you used to get from proccing your passive on 2-3 people at once is simply no longer possible. This leaves the ability feeling much less impactful than it was before.
The other use of Vel's ult is to proc your passive on 1 enemy with your regular spells and then ult that person for massive true damage. And in 1v1 scenarios, this feels more or less fine. But in teamfights, you're going to be proccing your passive on nothing but tanks and the occasional bruiser and ulting a lone tank just feels like crap even with the true damage. Vel's ult thematically screams that it's an AOE tool meant to melt entire teams but the true damage part of the ability is almost always used on only 1 person and that 1 person is usually a tank. And you're unlikely to kill that tank either even with a full channel of true damage.
And thus, you're left with 2 unsatisfying uses for your ult: use it how you did before, but worse; or use it on a tank and ruin the entire feel of the ability while also not even killing that tank more often than not. The ult change also makes Vel's possible combos far more limited since any combo that doesn't proc your passive before ulting is effectively wrong. Before, calculating just how many passive stacks you needed to apply before ulting to get the kill was a very important skill on Vel'koz and gave him a high degree of unpredictability, but now ulting at 1 or 2 stacks makes those stacks effectively worthless. It also doesn't help that Vel is just plain weaker than he was before: Winrate in Plat+ is down from 53.5% to 45.5% if LolKing is to be believed.