Abso-tooti-lutely some of the big third parties and the indies hold strong grudges or general feelings of resentment towards Nintendo.
A common theme is being treated very kindly and warmly by one representative for a few years, after which this person moves on to a new position or otherwise disappears, and the new contact you have access to treats you like a complete stranger, and as if you're generally of lowest possible priority.
For people like Ubisoft, EA, ActivisionBlizzard, and the other big boys, I'd suspect a key ingredient for resentment arriving in the form of a complete unwillingness on Nintendo's behalf to offer these behemoth companies any special treatment at all.
They're likely being asked to pay the same royalty percentage, the same server maintenance fees, and and the same cartridge manufacturing prices as the indies and smaller publishers like say Curve Digital or Team 17.
On top of that, Nintendo doesn't seem to allow publishers to demand that players create user profiles with them, AND Nintendo's ideas about microtransactions and DLC are visibly (and thankfully) conservative and counterintuitive to finding innovative ways of squeezing players for money.