I'm honestly curious. 

One has a imploding 1st party, the other a 3rd party relationship that would be a surprise to resolve even if Playstation and Xbox vanished one day completely and it was either Nintendo, PC, or making their own consoles. 

Who has the trickiest road going forward?

Pretty tough.
To be honest, I imagine both are still in better financial condition than Sony but Sony still has the sales and the support. As far as getting support from customers, I'd say Microsoft is always doing worse in the eyes of gamers, even when they're doing well.

Nintendo's greatest enemy is themselves
Microsoft's greatest enemy is Sony

It is obvious who is in the trickier situation here. One Company has to discipline themselves while another has to fight a multibillion dollar company.

So Microsoft
Also hint 3rd parties do not determine a Nintendo console's success.

In my opinion, Microsoft is in the worst position. They don't have enough first-party products to stand out, and most third-party offerings will go to Sony as well unless MS puts out the cash to make sure they get them first. Nintendo needs to sell hardware more than software, since their software is all but certain to sell tons.

Microsoft. Or more specifically, Microsoft's X-Box division.

Nintendo is a company with a pretty clear vision. They're going to be a company that develops games for the foreseeable future, and unless there is something absolutely catastrophic (like 3 Wii Us in a row), then they're going to be in the hardware business until if an when the market changes to make dedicated hardware irrelevant.

The XBox division on the other hand needs to justify its existence. Gaming is a drop in the bucket to Microsoft, and they're not devoted enough to stick with it through tough times. If it wasn't for Steam having such a large presence on PC, they'd probably be much quicker to transition "XBox" into a service. If the next XBox console isn't a lot more successful, I imagine that'll be it for the brand in terms of hardware.

*Stands*Clap clap clap*Looks around*Sits*

Well, Nintendo currently has the best selling console on the market. How tricky can that position be?

MS had the biggest problem: no real plan for the Xbox brand.

The answer is obvious.

One has a new console that is currently selling like hotcakes, and an uncontested GotY contender.

The other is slowly exiting the console market over the next five to seven years.

Xbox. Switch is doing well and they have 3DS to fall back on. They are opening a theme park soon. Nintendo can control their own fate. MS is part of a bigger entity that can determine if they still want to be in this market or not..Sony is stomping them in sales and exclusives. A $500 console will fill a niche need but it's not going to make Xbox suddenly catch up with PS4. MS has no market in the east.