I've followed the Robotech series for many years, mainly long after it's heyday. I got started when Del Rey released two omnibus re-printings of the first six novelizations by "Jack McKinney" (Brian Daley and James Luceno); I plowed through the contents of those books, enthralled with the Macross saga.
I have the whole series on DVD, including the Shadow Chronicles, and I also have all the books. The great thing about some of these properties is that there can be found a rich supply of story material in alternative media: Transformers had two continuities develop side-by-side in comics and the cartoon series; it's the same with G.I. Joe (and the Joe comics started several years before the cartoon gained momentum). You have to make allowances for the fact that some things just don't gel together, but in the end each production is just a different set of writer's and producers playing with the same toys in different ways.
The Robotech novels, although somewhat controversial, goes to great lengths to unify the three sagas even more than the superficial allusions thrown out at random here and there during the course of the cartoon. The cartoon is clever to an extent, the way it unifies three entirely separate anime series together.
Despite some elements in the novels that fans object to, five of the books cover the details of the Hunters' Expeditionary journey: the Sentinels series. These books can offer, at the very least a version of the events that happen. It won't match up with some elements that the Shadow Chronicles hints at, but then ask yourself how much the Star Wars prequels match up with the original SW trilogy and that can help you gauge how much divergence you find acceptable.
The original "final" Robotech novel, book 19, The End of the Circle, you can think of as a completely alternative version of the events that follow on from the end of the Mospeada/Invid War section of Robotech. An alternative version of The Shadow Chronicles. It takes a lot of the same players and set up, and runs them in very different directions, and heads toward very different outcomes.
I like The Shadow Chronicles for it's open ended nature, leaving the way for more stories and more questions. By the same token, I like The End of the Circle, which is an epic concluding volume of a massive multi-generational saga. It doesn't matter that the book isn't considered "canon" by some fans ("canon" is in some ways used as a bullying word to strong-arm fiction into the realm of apocrypha); ten or more years ago I read it and gained the satisfaction of experiencing one possible endpoint for the Robotech saga.
In a similar way, G.I. Joe has taken on new life for me, through the medium of the old, classic comics. I never read the old Marvel Joe comics, but I started when IDW began reprinting the old series. I've revisited all those old favorite characters, and been re-introduced to them (including some of my own action figures) in brand new ways. The comic continuity cannot be matched up with the old cartoon hold my original memories of what G.I. Joe was like, but that's okay, the story and characters have been revitalized in a vibrant way. I will not speak of The Rise of Cobra movie, though, which I found very strange and unsatisfying...
Returning to Robotech, it occurs to me that there's a lot of material to the story, and pushing the universe forward with a new series while remaining user-friendly seems like a daunting prospect. How do you revitalize Robotech for new and old audiences, while spring off from The Shadow Chronicles endpoint? Robotech might be overdue for a return to it's beginning...
I know there's a lot of talk and backlash against wave after wave of re-booted franchises, but I've only seen two properties which are questionable: the Spiderman movies, and the Superman comics. The first two Spiderman movies were great, and I think a lot of people forget that fact and give the third Spiderman movie too much weight as a franchise-killer; you just can't compare Spiderman 3 to the devastation of Batman Forever and Batman and Robin as justification for re-starting the story. Disappointment notwithstanding, I am looking foward to The Amazing Spiderman and hope it will be fun. As for Superman, I find it odd that they felt the need to do an origin story only a very short few years after Birthright cleverly conceptualized Superman to open up more broadly the storytelling possibilities for the writers while telling a great, emotional story; a cursory appraisal of Secret Origin suggests to me it is superfluous, questionably paced, and a bit silly IMO. But, I digress.