I think the hardest thing about being independent is learning to be your own boss. When you first start off, motivation is high and it's hard not to work on your game. But as time goes on, it gets harder and harder to get as excited about working. You begin to realize that more-so than motivation, you need dedication to keep working.
Having a team or partner makes this a lot easier. Partners keep each other accountable, and it's a lot harder to put off work when you know other people are expecting you to get it done. It's also really motivating when a partner commits significant code or has some new art to show off. I find that a common pattern when I work with someone else on a project is that we cyclically feed off of each other's work.
Sometimes though you just have to sit down by yourself and get work done. I haven't figured out a magic solution yet that'll allow me to work consistently for long hours every day, and I'm not sure if there is one. Caffeine helps. For the most part though, I alternate frequently between working hard to the point of near-burnout and taking time off.
Nuke Nine is only the three of us for now. Despite our small size, it can be hard to make sure we're all on the same page. Part of this could be due to the distributed nature of our work; I've never actually met Keo in person. But I think making sure any team communicates well requires significant effort. We use Google Hangouts to hold meetings and to come to decisions, which works pretty well for us.
I think it's easy to underestimate the value of meetings. A somewhat common sentiment among programmers is that meetings are a waste of time. Why pull someone away from their work, interrupting their flow? I can sympathize, but every meeting starts off with a specific intention or goal. Sometimes the goal is met. Sometimes it's not. Luckily, I think having effective meetings is a collaborative skill that can be developed. It's amazing how incredibly easy it is to talk for an hour, agreeing with each other and ultimately feeling good about the talk, without actually getting anything done. Having hard goals before a meeting can help make sure no one's time is wasted.
As a team, we're still developing this skill; but we're getting there.