We just moved into a new house that had good condition standard oak floors, but that usual orange colored stain.

Here's a before look:

My wife and I really wanted that dark wood look.

Inspiration Room:

Based on the floor sample stains we saw, we chose Jacobean.
KEY: far left (Special walnut), Middle top (Special Walnut + English Chestnut), Middle center (English Chestnut), Middle bottom (Ebony + English Chestnut), Far Right (Jacobean)

The first coat of the stain was not anything close to what we wanted.

Hallway 1 coat of stain:

Family Room 1 coat of stain:

I called my flooring subcontractor, and told him its too light, and to put another coat of stain down, much to his annoyance. Here's the result:
Hallway 2 coats:

Front Hallway 2 coats:

Living Room 2 coats:

The flooring guy was telling me the color will richen a bit once the 3 coats of water based sealant are put down, and it'll even out. I'm so torn what to do, my wife is not happy at all with the color, and with how much grain shows through.

Is what he says true? Should we get him to do a 3rd stain? With a differen't color perhaps? Or is this the nature of standard oak floors, that they will always have the grain come through like this?

From what I am seeing there is no amount of poly which is going to get you two the color you want. Did your flooring guy see your inspiration pic? If so, is he color blind? There is NO WAY that color in any way, shape or form resembles your inspiration. If you're set on Minwax I'd probably suggest going like 40-60 Ebony Jacobean, or even 50-50 -- straight Jacobean is not going to get you the depth you're after.

We have red oak and wanted that dark look: red oak is notoriously difficult to get to the chocolate color, so my sweet husband did a ton of research and found that DuraSeal Penetrating Stain, and we used Ebony 231, was the way for us to get the deep, rich color we wanted (many of the pre-war apts in NY have red oak floors and this was their magic ticket to the ebony color). This was nearly five years ago so I'm sure other stains have improved their red oak abilities as well .... But first the wood had to be popped by soaking it in water -- that allows the grain to open to absorb the color, and in our house, the deep color.

I'm not finding an ideal pic to share so I'll post a couple:

The floor and its color look pretty flat, but in real life they have more depth:

And in this pic you can better see the grain, although due to the flash it's ultra-highlighted here (doesn't look like this in real life)

I'm so sorry, but I think you'll really have to do more stain, but let's face it, now is the time to do it and do it right, because I promise you'll always regret it if you don't. We were living in another state when we purchased this house and had the floors installed (and stained). Even with e-mailed inspiration pics, our flooring guy came up with this color:

and it was wrong. We only discovered how wrong it was as we were moving in. So one year+ later, we moved everything out and had them redone. Pain in the rear? You bet. Worth it? Absolutely. For the record, our flooring guy had used Bona's Ebony stain, but I'd hardly call that color ebony, would you?