Quick First Impressions Review of the Two Sites Compared to Each Other:
If you can only pick one:
Pickup Music. Has more to offer at a cheaper pricepoint, is far more user friendly. The lessons are bite sized, you can pick up the basics of a new technique pretty quickly with application and practice, it offers more than just guitar ("piano for the guitarist," is one course they have, for example, as well as "vocals for the singer/songwriter"), so you really get a lot of value for the money.
If you want a deep dive into theory:
Guitar Super System. Tyler has basically put Berklee's entire music course online for a tenner a month. I mean, that sums up the entire thing right there. that's the GSS. Berklee Music School's Online Guitar Course, but with Tyler from Music Is Win as a teacher, and more approachable.
Community:
Both have fairly active forums, but GSS's is more in line with a traditional online forum. Pickup Music is kind of haphazard, and the notification system isn't all that great. The people in both communities are great, though. Replies are usually pretty swift.
Format:
Both use video/tab to teach. Both have standard notation. Pickup Music has a course on learning to sight-read, so you could end up using something like lead sheets down the road.
Overall Impressions:
Both are excellent systems, both can be used by beginners or advanced guitarists. I would recommend Pickup Music for improving your overall skill, and GSS for your technical ability/music theory.
Will I Resub to Either/Or/Neither/Nor:
I will maintain my sub to both. They are amazeballs.