Mrstarker: Even if we accept that there is a First Cause, which is debatable, it does in no way follow that this is God, or that this is intelligent, or a perfect being, or that it would interact with the universe at all.
I hope you realize that Aquinas does deal with these topics in the
Summa Theologica and that the First Cause is a summary argument. Also, it's nonsensical for there be a First Cause that doesn't interact with the universe at all, that's kind of the point of being the cause.
Mrstarker: The argument from design just seems flawed anthropocentric thinking. Aristoteles himself rejected this, if memory serves.
If you think he is using anthropocentric thinking, then you've misunderstood him. He is saying that final causality is evident wherever some natural object or process has a tendency to produce some particular effect of range of effects. For instance, striking a match reliably generates heat and light and not frost or lightning, so it is inherently directed towards that specific range of effects. Unless a cause were inherently directed towards an effect or range of effects, then there would be no particular reason why it should bring about that effect or range of effects.
Furthermore, it is unwise to apply observations from our own small corner of the world to the universe at large. Things work way different on the quantum level, so why would we assume that they are the same in the other extreme?
"Everything that begins to exist has a cause" is a statement that is self-evidently true. There's no reason to think that it is false or to expect that we ever will find reason to think it is false, so I see nothing wrong with building off the premise until we do. Assuming a particular theorem in quantum mechanics is correct, at most it tells us that there is something with no physical, but it unable to rule out the possibility of nonphysical intelligent causes. Considering that that is what Aquinas is setting out to prove, to assume there isn't one is begging the question.