Okay it's been a long time since I posted here but thanks for this thread because (1) I'm a Strat player right down to the bone and (2) this is something I might as well have posted myself had I been active at the time it was relevant to me. So here's my 2 cents on setting up a Strat:
This probably isn't quite what you want to hear, but I find a Strat sounds better when you use a medium action leaning towards slightly high, that's how I find I get the best tone out of mine. I spent ages trying to set mine up with the lowest action possible to make it easier to play but I found I just got fretbuzz and intonation problems from it that way, so in the end I gave up and decided this wasn't the guitar to use when I wanted to practice picking scales up and down fast or legatoing up and down scales the same way. But I still loved the tone of a Strat, especially on the clean sound, and I liked the feel of both the body and neck better than any other guitar I'd found, so my compromise was it became the guitar I'd pick up when I felt like being a little more traditional and wasn't so hung up on trying to play fast or wanting the guitar that could accommodate every lick I know. A Strat also sounds rather nice with thicker strings and tuned down half a step (at the moment mine isn't set up for this but I've done it before and it's quite rewarding in terms of tone.)
Another setup issue I had with my Strat was the tremolo, to begin with when I bought it 9 years ago I wanted to have a really stiff tremolo so I went out and got 2 more springs so I had 5 loaded in there in total, but a few months ago I decided to try taking two of them out and seeing if my playing style would adapt to a lighter touch on the bar, and I found it so much better that I kept it that way. Of course I had to adjust the spring claw and the saddles to get the intonation right again but it was worth it. How you set up your tremolo (assuming your Strat has one) will affect how it plays, whether you have it floating or set up for bending down only (I prefer the latter.)
To sum up, keep in mind that what you're playing (and to some extent what you can't do yet that you're aspiring to learn) will affect how you want the Strat set up. As you haven't specified what you're into it's hard for me to advise.
'There's no such thing as bad weather, there's only the wrong clothes...'