Based on what people tend to joke about, I'd say Arzest is Nintendo's least competent developer.
Game Freak makes okay games, but I'd say that this is largely because they have a solid base on which to build their games on. When it comes to building on that base, they've stepped into a cycle where they don't actively try to make a better game than their last. Each generation introduces a couple of new mechanics that are eventually forgotten about when the next generation comes around; Triple/rotation/sky/inverse battles have been thrown away, Pokemon don't follow you, swarms don't exist anymore, hordes are gone, mega evolution seems to have been abandoned, contests came back and are now gone, secret bases as well, etc. I wouldn't be surprised to see z-moves fade away in the future. The games seem to be designed in a way where a new feature or two is introduced for that new pull factor at the expense of existing features which are brushed under the rug. Things that remain are sometimes done worse than in past games (Sun and Moon's menu system is a disgrace compared to X/Y's for example, while SOS'ing for hidden abilities is awful). They did a great thing by making HG/SS a complete improvement over the originals, with everything from Crystal included and much more, yet ORAS didn't even include Emerald's base content and featured rather anemic added content.
Additionally, I think their map design, story pacing, and complexity of the world (time related events, important NPCs, specialized areas) have all gotten worse over time. You would think that they'd have the money to find good talent to make a decent story when they decide to shove in cutscenes every 5 minutes like in S/M. They also haven't actually tried to push the systems they're on for a while now, which is kind of lame since they make the main games for one of the largest video game franchises on Earth.
I kind of wish Pokemon didn't experience the massive resurgence it did last year. Maybe it would have pushed TPC/GameFreak to actually put some time, money and effort into their titles (or maybe it would have resulted in more mobile games, who knows).