Considering their job with FF XIII Versus, KH3, FF VIIR and as you said DQXI, yes they have facing some big issues.

While hate is a strong word, you have to understand that companies are run by humans. We make mistakes, have bad judgement, underestimate numbers and other companies, even hold grudges. 

I certainly think SE doesn't hate Nintendo, or has anything against them. But they surely show a lack of confidence, at least in the early stages of Switch's lifecycle. That is also true for most 3rd parties. 

You know shit has hit the fan when the fiercest 3rd party Nintendo supporter is Bethesda, lol.

I think fan perception and reality just don't jive here.   Square Enix has actually been an enthusiastic supporter of Switch - since Day one.  In fact, they are one of the most prominent developers/publishers among the major companies thus far:

-Dragon Quest X (Japan only)

-Dragon Quest XI (Upcoming)

- Dragon Quest Builders

- Dragon Quest Builders 2

- Dragon Quest Heroes I & II (Japan only)

- Fear Effect Reinvented (as publisher)

- Fear Effect Sedna (as publisher)

- Goetia (as publisher)

- I am Setsuna

- Lost Sphear 

-Octopath Traveller (upcoming)

- Romancing SaGa 2

- SaGa: Scarlet Grace (Japan only)

- Seiken Densetsu Collection (Japan only)

- Spelunker Party! (as publisher)

- TWEWY: Final Remix (upcoming)

If I were to hazard a guess, it's probably a combination of bloated size and poor management practices due to too much micromanagement from upper level executives.  Rumors of the latter have floated around SE for a while now.  As for size, many assume bigger is better but it is commonly understood that larger teams are harder to manage and SE does tend to have some very large teams.  This issue of team bloat though is fairly universal in the industry today though, hence why seemingly simple projects tumble into development hell and costs have skyrocketed disproportionate to team size increase.

All I know is something has well and truly effed up when Wild Card Studios has an alpha build for Ark up before we have a screenshot of DQXI by one of the most wealthy and powerful publishers in the world :P

I call serious BS.  Imagine how the Sony fanbase would react if SE put a bunch of mid tier games on the system but no Final Fantasy.  Or how Sony/MS fans would react is Activision put out a bunch of games on their system but no Call of Duty or Destiny.  Or Ubisoft without Far Cry and Assassins Creed.  Or EA without Battlefield, FIFA, Battlefront and Mass Effect.

My point is you can't say they are the worst when they are the only ones that have to deal with it.  "Worst" implies other entities deal with it better. But if no other entity is involved, there is nothing to be compared to.  You could equally say they are the best at it.  Further, your tone implied frustration or derision at Nintendo fans for wanting popular games.

Really? 

The user I qouted is right. Perception and reality just dont jive here. If there is anything that frustrates me it would be support begging, without actually supporting the great games that you already have available. The success of the Switch is not by Nintendo fans. It could never be. Too small of a box/range/taste. If from average gamers who buy games, unworried about Ip recognition"heey CAPCOM did that there but not here waaaah". They dont care.

 Ikaruga came out - How many people bought it?