There's a lot of speculation and external observation going on in here, so I'll just briefly offer my perspective as someone who is actively trying to work their way into the world of indie development. This is just my own experience and opinion, so I'm sure it's not representative of other indie devs. I'm also going to omit most of the details (names, dates, numbers, etc.) because it wouldn't really be professional of me to speak to those.
The biggest advantage that Sony has over MS with regards to indie games is the way they're extremely active in courting interesting projects as they pop up. If you have an indie game that's getting some significant amount of attention via social media, there's a decent chance that someone at Sony will initiate contact with you. From there, it's an extremely low friction process to start working with them, and the people at Sony are very helpful and nice at every step along the way.
Maybe this is just me, but that extremely pleasant interaction kinda engenders a sense of loyalty. It feels like Sony has genuine confidence in your product and wants to help you make it successful. That sense of loyalty is a bit contagious, and I think it plays a huge part in making other developers and people in general feel encouraged by Sony's approach to indie games.
On the flip side, regardless of how much of it is actually truth vs perception, everything about approaching MS feels like trying to get inside of a walled city. Unless you have a massively popular up and coming project, it doesn't seem like MS is really initiating contact with any devs. You're most likely going to need to go pay the fee to become a registered MS developer and then submit to ID@Xbox without any prior interaction from someone at MS. It's not a hugely involved or costly process, but it ends up feeling like you're paying a fee for the opportunity to cold call and sell someone on your game. It's still relatively low risk to apply, but any amount of friction at all just makes it feel like much more of a long shot than the Sony experience.
I've only ever had one brief conversation with someone from ID@Xbox because I met them in person at GDC, and I didn't walk away from it feeling any better about the prospect of approaching an Xbox One release. To be totally honest, I felt like I was kinda being guilt tripped into applying. The conversation mostly boiled down to, "We've sent out X dev kits to developers. Don't you think you're one of the top X developers out there? If you don't fill out the application, you'll never find out what it's like to work with us." (just paraphrasing here, not an exact quote)
This isn't even touching on whatever MS's contractual obligations are with regard to release parity or additional content - I don't actually know about any of it and wouldn't be able to say anything specific if I did. I'm sure a lot of it is negotiable and won't be the same for every developer anyway.
Nintendo hasn't really entered into the discussion in this thread much, but for the record, all of my interaction with them has also been very pleasant and productive.