I don't think that the second system effect applies, specifically given that it isn't elegant or successful yet. (In fact, most of the comments are that it is inelegant and a failure).
Second system effect mostly reflects the evils of redesigning a perfectly good working product.
(Debugging is 90% of software development).
But this isn't even debugged.
I write a prototype to learn the technologies for a given project all the time. It is the first step in my development cycle (How the hell does this stuff work?) I don't design it, I just start hacking.
Once I have an understanding of how the various pieces are able to fit together, then I make a design and put together the first system.
My point is that I don't think this is complete or well-implemented enough to comprise a first system. (And it isn't, it is an alpha).
IMO, second system effect is doing everything you've done bigger and better while fixing the problems in the first system. It wasn't tied to the elegance of the first system design, at least in my mind.