To be clear, Nintendo has had weaker periods in Europe. The NES, SNES, and N64 underperformed there.
The bigger problem with Fifa is that the Switch version is universally recognized as objectively inferior to other major versions. That it looks a bit better than the PS360 version as EA declares doesn't change that it is missing the big new feature for the game. As a result, I've seen a lot of rolling of eyes with regards to Fifa. Skyrim, on the other hand, has had a pretty good reception. It looks like a much higher effort port, is feature complete, and seems to be at least derived fromthe Special Edition release. I've seen much more positivity with Skyrim. And the title could very well experience some synergy with Zelda as a lot of people who loved that game and loved having it on the go may be looking for a similar experience.
Honestly, a better comparison would be NBA 2k18 and Skyrim, two feature complete and good effort ports.
The vast majority of Nintendo home consoles never went big in Europe but at least their brand presence was made up with their portable systems since the SNES and onwards ...
Portable versions will practically always be technically inferior to the home systems and that comparison also applies to Skyrim too with Switch vs PS4/X1 versions and sometimes there's content cuts too when doing home system to portable system conversions since there's not enough storage space for portable systems or other technical limitations ... (Portable versions usually have different artwork as it is so what's the issue with different content ?)
It cannot be denied that Skyrim will undergo a second rerelease whereas FIFA 18 is a new game that won't have all of the features included in all of it's releases ... (Heck, the PS4/X1 versions of FIFA 18 doesn't have local multiplayer whereas the Switch won't have journey mode so it works boths ways plus Skyrim on the Switch is a technical downgrade from the PS4/X1 versions just like FIFA 18 is on the Switch.)
It's not the technical gap that's the issue. It's the fact that Career Mode and Ultimate Team are more limited and The Journey is cut. And unless an EA dev comes to my house and proves otherwise, all evidence points to this being a result of EA being cheap, not the Switch being unable to run a soccer game - a freaking soccer game - on an engine designed for the PS360 in the first place.
In short, the game is feature stripped. Gimped. Objectively inferior in ways beyond simple graphics. And that stigma will hamper it. Do your casual Fifa players know all this? Nah. But that's actually worse. All your casual fans will hear is "the game is feature stripped" and boom. Done. That's it. Sale lost. Some will value the portability enough, most will not.
And the PS4 and Xbone versions have normal old local multiplayer. I doubt the ability to play system to system local will even register on the radar.
Skyrim is technically downgraded but at least noticeably stepped up from last gen and includes all the DLC plus some added trinkets. That is, it is a full and complete version of the game + portability. Not a feature stripped version hoping for portability to offset it.