Why bake bread from scratch? Why not buy a loaf?
I think the best way to answer this is with a similar analogy. Let's say you go to the salad bar at your local grocery store. You want tuna today, so you scoop some into your container, go to check out, and proceed to enjoy your lunch...but wait...there's a lot of mayo and it tastes really fishy (I know it is fish, but other ingredients help to lighten the flavor). Turns out you didn't like it that much.
So you go back to the grocery store. This time, you purchase all the ingredients you want, you go home, and you make your own tuna...this time, you find that it's absolutely delicious by your standards! What's more, you have enough to last for a few meals rather than just one.
There's nothing wrong with the pre-made tuna in the store. I imagine many people enjoy it. But what about the people who don't? How many other people prefer the sweeter, creamier tuna you just made? That's your target audience.
Long story short, you could use Unity or Game Maker to make your games. Many people enjoy games produced from those engines. But there are also many people who would prefer a change of pace or just something outside of the norm. You could modify the pre-made tuna you purchased earlier, but you would have to consider the ingredients that have already been added, and if your own ingredients would work or clash with what's already there. It's easier to start from scratch, in this case, because you will know exactly what goes into your tuna (game).
If that was confusing, I apologize in advance.
A little story:
When the Wii launched I was working at a games company that had a lead programmer who insisted on writing everything in house by the time we had finished writing an cross platform engine to support Wii, DS, XBOX360 and PC (we didn't do PS3), an in house scripting language, in house exporters for MAX and Photoshop, an in house shader language and in house physics engine the Wii was pretty much obsolete and all the publishers had already started to abandon it. The publishers who saw our products said that they were some of the most amazing games in the Genre that they had seen on Wii hardware but that they could not fund because the Wii ship had sailed.
Most of our competitors had used things like Gamebryo, got publishing deals early and shipped games in less than six months. We all got made redundant.
It seems to me that your story proves the value and usefulness of writing your own engines from scratch. Some of the "most amazing games" they've ever seen? Wow! Clearly, the issue was that your team didn't finish fast enough. I wouldn't write myself off like that just because I didn't make it in time. If the team had, it would've been quite successful!
In any case, I wonder what could lengthen a project to a degree that extreme anyway. I mean, the Wii was popular for quite a long time after it was released in 2006. I think the issue was that the team wasn't focused on the Wii alone (Shouldn't porting come later?).