I don't see Subgenuis as anything other than a parody religion. Discordianism is a little satirical in areas (albeit in a fond manner) and humor is a vehicle for conveying important ideas, like in Zen. Discordianism knocks Occultism and Religion but always strives to push past that. The principle of Greyface is at the heart of Discordianism I believe, it poses that the overemphasis on seriousness, both in religion/occultism and in general life - is the thing that perpetuates delusion, cult-behavior (which happens in the secular world too) and is ultimately a distraction. Of course, life is about balance between seriousness and humor, too much of either is a bad thing.
Discordianism has many hilarious inside jokes and in it's nature, feeds of memes. It provides a framework for absurdist anarchy, it provides guidelines of how to approach your own spirituality, it has it's own magical rituals and Mindfuck Orders. Robert Anton Wilson certainly saw this in Discordianism too and it shows in his approach to his own syncronistic adventures.
Even though Bob Wilson was also entertained by the Subgenius, I don't find much value in it outside of it's basic parody-value.