Microsoft CAN build a prescence in Japan, but it would take a lot of things (and money):
First off, they would have to buy some Japanese studios. Not smaller developers, like Mistwalker I'm talking bigger developers like Level-5 and Sega. If they want to do more in Japan, they would also have to steal top talent away from bigger publishers like Nintendo, Square Enix, and Konami. With the talent they would need at least 2 studios with about 75-100 people built from scratch.
They would also have to spend BIG $$$ buying eclusives like Nintendo did with Bayonetta 2. Monster Hunter and Dragon Quest are locked up at the moment, so they should look at other franchises like Tales of ___, Dynasty Warriors, Professor Layton (Level 5 owns the IP, so it could happen.), or even Final Fantasy, if they DARE.
Next, they would have to scrap the Xbox brand completely. The Japanese typically buy Japanese, so they should rename their Japanese branch something completely new. They should abandon the MS name completely. The next console should also get an exclusive Japanese design like consoles past, and not be too big or anything like the original Xbox.
Sony isn't doing well in Japan right now, so if MS makes a big enough splash next gen, things would get better for them, and worse for Sony.
