I used to have a Sealife and strobe setup - during a trip to Indonesia I got so frustrated with it that the first thing I did when coming back was sell it and order a Ikelite housing for my 20D (and two DS125).
The main advantage of the sealife is bulk. You can still tie it somewhere and forget about it for the rest of the dive if conditions aren't good. That's not really possible with SLR and strobes.
The second advantage is wet lenses. You can switch from macro to wide angle underwater, while with the SLR you need to decide in advance. Obviously, it's when you load for whale shark that you find pigmy seahorses
Now, when you're actually doing photography - the SLR is incomparable. With TTL, flash exposure is always spot on - the modeling lights are great, the strobes recycle in 1 to 2 seconds, there is no shutter lag, no fog, autofocus works great even in very low light, you can mess with DOF if you wish... Bottom line is, you have full creative control over your photos (and can take a ton of variations FAST - even with strobes) instead of having one shot every 10 seconds and hopping the Sealife takes the right decisions for you.
For lenses and ports - my setup is:
- The Canon 60 macro with standard flat port (my profile photo is with that setup). In very rare occasions (pigmy seahorses?) I wished I had a 100, but the 60 still allows to shoot fishes and larger stuff if the small stuff is a no show.
- The Canon 10-22 zoom with dome port for wide angle. Lens is good, but I still suck at wide angle composition :depressed:
- The 18-55 with the flat port when I'm not sure. I have a 'better' 24-85 which fits in the port and that I prefer for land use, but I prefer the range of the 18-55 for underwater.
I had all those lenses for land use already.
Honestly, I don't have any experience with other lenses/ports combos, so you'll want to do more research - but I'm happy with mines.
For protection of your investment, I use and recommend DEPP. I don't know if there are others now offering good conditions, but at the time I bought my gear that was the way to go (DAN conditions weren't that good on photo gear).
When I travel, it has its own pelican case. I stopped worrying about it and rely on my insurance if it 'disappears' between two airports.