I treat them as separate entities, and therefore feel no shame or hesitation to say that I like them both.
Robotech has a more epic and coordinated feel to it, simply because it has been filled in so well. All the same, though, it can't avoid the awkwardness that arises from the bastardization of storylines....
Macross I like because it makes more sense overall, and has a clearer view of humanity struggling with what it inherently has against hostile outside influences. It does have it's own continuity problems, though....
Frankly, I collect both Macross and Robotech stuff, have always and will always. I just treat them like two different series....