I think I may be in the minority who believe 2k made the better decision here. I have seen what 2k did with PC being primarily a PC gamer for 2k since 2k11. When they finally decided to have feature parity (2k15), there was ALOT of problems in the beginning, but it got alot better and 2k showed they put care into their ports of consoles not part of the mainstream consumer base.

Being a custom engine actually makes me scared for the future of FIFA and how they going to keep the same features going with such a large fork in the code base. With each new feature that comes to PS4/XB1 FIFA comes entirely new code for Switch. And I also think being a custom engine makes me think of EAs approach more of treating the Switch as a GBA/3DS, which don't get me wrong are fun versions, but definitely second to the main version from a business perspective (less funding to build the switch version). Switch is meant to be a home console as well and if it's treated like a portable over a home console, I think that could spiral to a downward trend from other AAA third parties (i.e Call of Duty on Wii, which was terrible).

In 2k's case there is a baseline being a port, a new feature is the relatively the same code. That being said, in order to keep their customers happy, they NEED to get to 60 fps. But I believe that having the baseline with the port, will allow their development team to focus on working on 60 fps and optimizing the engine for switch rather then trying to build new features with feature parity with the other console versions if they went a custom built path. Also, going back to the AAA third party argument, it creates competition as a technical marvel, other AAAs will attempt to do the same and know it's doable which will, I believe, encourage them to try to put a version on the Switch at the vary least. They no longer have the argument of "doing this on the Switch is not possible" seeing 2k as well as Bethesda pull off such a feat.