Having trouble would probably be a bad term to use. More like I don't think they were really prepared for how time consuming and expensive HD development would be. It'd part of the reason they have this expansion coming to their main building soon. If I recall isn't Namco working on smash because they wanted to get with someone would had experience with HD development,.
I think we take as gamers look at Nintendo and wrongfully complain about them not having more. The problem is that the majority of the Industry is working on has stupidly oversized teams and reuse assets (Assassin's Creed, FFXIII).
Even the bigger mainline titles take a good amount of time before the next one comes out. It was six years between Halo 3 and 4 and the development time was around 4-5 years. I'm expecting another big wait between H4 and H5 as well. Assassins Cred had a 3-4 year delay with all of its main series. We just get those side games because ubisoft loves its vitamin D.
But for some reason nintendo who also follows this type of schedule is considered bad.
The only real thongs that were disappointing about ND to me were Mario Kart so soon and the fact that the NSMBU dlc wasn't announced.