I don't know if this matters, but what twigged me on your question was the "...in the long run?" part. If you're new to both diving and u/w photography (as I pretty much still am - 80 dives but that's "new" compared to most folks here) its a pretty sure bet that you dont' KNOW what you want for "the long run". In that sense, my advice is to save some money and experiment, which probably means Ikelite has a lower entry barrier. A lot of people say "why chase upgrades, buy 'good stuff' the first time", but how do you learn if you haven't tried? My guess would be why not just house the camera you've got now?
Then again, if money is no object, erase the above. And earn my instant hatred.
Kidding! But seriously, you can get an Ike housing with TTL included, and an 8" dome and port extension, for the price of just the S&S housing. The housing is a sunk cost, since by the time you upgrade it is unlikely to find someone else to take it off your hands (unless you like upgrading in very short intervals), but the ports are re-sellable even if you switch systems, ditto the strobes and sync cords. I speak as one who is shooting with a used housing, used ports, used strobes, used cords, and even second hand strobe arms! Only my camera primary body was bought 'new' (yep, got a used backup body too).
I don't know enough to have a strong opinion about strobes one way or the other...I am using used DS50s right now as my cheapo entry point. (Refer back to the hatred bit above...heh...) I would recommend they're a bit small if you want to do W/A...so at the least go with the DS125 or equivalent-sized S&S strobe.
Ike housings are a bit unstreamlined and fugly perhaps, but they work just fine, and behind an 8" dome and dome shade all housings are more or less the same for swimming with I bet. Underwater they're nearly neutral - don't know if the same is true of smaller housings that trap less air (again, dome port is probably the bigger modifier for actual in-use weight) and are made of aluminum which can be thinner than the acrylic for the same effective strength. The bulk and weight difference of the housing are kind of negated by strobes and strobe arms anyway - no matter how 'small' the housing itself is, once you put handles on it and create a mechanical spider you've got about the same sized obstruction underwater to swim with. If you neutralize the buoyancy either way, it's probably a tossup as to the added swimming effort except in the most raging currents.
I don't have a strong personal opinion about "clear lets you see seals and look for leaks" vs. a leak detector/alarm. I have an Ike and frankly you can only clearly 'see' the main body o-ring, on the rear face. The other face is too hard to see (if you're talking about inspecting for hair, sand, lint, etc) thru the curvature of the housing. The port o-ring is too hard to see around the dome and housing unless you can inspect it somehow before sealing the back, and the focus ring gear assembly sequence kind of negates that ability. Underwater it's very easy to see if you have water rolling around the bottom (thank Neptune I haven't yet!) but I don't see how that is 'better' or 'worse' than a leak alarm. Either way I'm willing to bet you're only going to escape with minor injuries in cases of extreme luck.
In terms of which housings I've 'seen' on other trips...mostly small OEM housings. In the Flower Gardens most of the 'pros' seem to have the huge banged up old gray Aquatica housings, with a smattering of Olympus branded OEM housings. On my recent trip to Dominica my Ike was the big daddy of the bunch - among 18 other divers total, no one else had anything bigger than a digicam, although one guy's non-diving wife had his 40D for shooting from the boat on the way out. He kept hanging around my rig like a hungry puppy, even though his camera is much higher end than mine, mine was HOUSED.
I guess it would be different if I worked for a dive photo shop and sponsored trips specifically for photographers. Wouldn't you then tend to just see the housings you sold since the divers would be mostly your customers? 