I think the initial choice of LSA is probably more important than the difference between a certified and non-certified version of the same thing. That said, I don't object to having a tighter-tracked product. As you'll know though, it's entirely possible to run a GA registered LSA version but I have no data to tell me whether the reliability is better/worse than my EASA VLA certified model.
They are the pretty much an identical aircraft as you would know; it's just that LSA is a little scary as to what can happen in terms of the paperwork. When the factory goes bust someone needs to own the C of A and if that doesn't happen, you are grounded in LSA. I heard that Fly Synthesis went under recently, which could potentially mean that owners are grounded in 30 days from then. A properly certified version gives added reassurance. If it's a half-baked LSA from some Euro country that didn't sell many of them, kiss your LSA status good bye and bye-bye flying school revenue from that aircraft.
I would say you made the right choice with your aircraft purchase
Is yours the one where the backing plate on the tacho has been changed to only show max 3,000 rpm? I found that quite interesting.