It's quite easy to find depth in many things...
Whether or not the 'depth' is well constructed and endearing is the key. Endearing being the most crucial. Shows I watched as a kid (I'll throw one out there) like the Rugrats is purely a kids show, but of course the depth is the underlying 'adult human' that the kids won't pick up. That same depth is in many 'kiddy' things, usually as comedy.
On the other hand many shows directed at a younger audience generally all revolve around delivering ideas and morals (i.e. OMG ASH KETCHUM FOUND A WEAK UNCARED FOR CHARMANDER AND SAVED ITS LIFE, NOW IF I SEE SICK ANIMALS I WONT LAUGH AND WATCH THEM DIE).
What Gainax are really trying to say here is that us is that (supposibly) the depth of GL will be revealed to us in many years after many life experiences. I don't know which demographic they were aiming those comments, but the next 'big change' for us is the mid-life crisis... Will we really see GL in a different light then?
Just like how we see other kid shows of our youth in today's eyes as "wow, never noticed that", the same will probably be for GL for a younger audience. For us, maybe not.