The S40 should be a perfect size for you and very manageable. Don't know about the S50 but I assume it's heavier, maybe a bit faster. Probably work good, too, though a little less easy to handle for commuting, maybe a bit better for interstate/highway.

S50 is a better bike. Has longer life, has more power, fits the common understending for a bike , it is V-twin,has better brakes, so overall it is more of a bike. I've had couple of them, and I still have one and I am selling it.
And after I said all of this, I'll say that I ride my Savage every day, I enjoy it more, I have way more fun on it, and I am NOT selling it.
To work on a Savage is a walk in the park, compared with work on the Intruder. If You have a GOOD mechanic to tune the carb's the Intruder runs SWEET, but there are not too many guys who can or who will care to do it corect.
If You will carry a person behind , may be the Intruder is better.
If You are talking FUN, I think Savage is the way to go.
Like an investment, I think it is about the same, but the Savage seems just a little better /I might not be right/.
If it was me, I'd watch for somebody in his midlife crisis, who bought his Savage couple of years ago and put 1000-2000 miles, and now he just wants to get rid of it, and I'd snatch it for about $2500. After that will ride the hell out of it and will sell it for about $2000.

The S50 will give you more power and aftermarket support.  The S40 will give you superb handling and as little weight as possible.  Neither one should be a stretch for you at 5'6" and neither one is a particularly heavy bike.  The more interstate you do, the more you'll want the S50, I think.  The more winding roads you do, the more you'll want the S40.  

Like Slavy said, the Savage/S40 is a piece of cake to maintain and customize.  The S50 will take a bit more work and upkeep.

I think you'd be happy with either one.  Take the one that appeals to you the most.  If you don't get the one that most gives you that special gut feeling, you'll be second guessing it the entire time you own the bike.

You might consider dropping by http://www.intruderalert.com/ and talking to them a bit.

In a perfect world, you could have both.  

Have one of each at home.

The Savage gets better mileage, handles better, rides better, is faster, and costs much less to buy/maintain/operate.

The Intruder sounds better (if piped properly, stock sound is horrible). Intruder seat sits better, but the cover is lower quality. Comes with non-adjustable handlebars, set up for internal wiring. Same lights as the Savage (cheap).

You are in the right height range for either. Test sit both, test ride both if you can find a metric dealer who allows that (extremely rare these days, non-existent where I live).

Like previously suggested, check out IntruderAlert.com, find a guy named Polar Pilot, and talk to him. Went from Savage to VS1400, which is the same chassis as a VS800.
-WD