With a dome on I don't think smaller matters much. For me it would come down to price! At Reef Photo the Naudicam is $2800 and the Seatool $2999. I think that one should also check out port availability and costs since the housings are within $100-200 of each other. I happen to have the 180 degree INON viewfinder ($900) which moves the Seatool (Reef Photo) to $3800. I assume that you can add a magnifing viewfinder to the Nudicam also. Bottom line I would call Ryan at Reef Photo (He is the Nikon guy. Richard is an Olympus puke and Kelly is Canon) and ask.
For macro and shore diving the smaller housing is slightly superior. For example The Naudicam appears to have dual handles built in. The Seatool, otoh has a built-in ball mounting. With a single strobe macro setup I can go without any tray at all, mount a single strobe on that ball and use a hand strap. Alternately, I can mount a single arm and use two strobes, attaching the focus light to the strobe mount if I want to. Overall i believe that the Seatool an be a smaller package.
I was able to get a 17-70 Sigma to mount in a flat port (the zoom ring is permanantly attached to the 17/70) so that I could take decent midrange shots (near macro to near wide angle) but I have not yet invested in a dome. My compound ports will support the Sigma 17-70 (needs a flaired flat port), Af-105-VR, af-105-vr+ 2:1 TC and a 60mm.
Adding a dome would be trivial (I have a 12/24) but IMHO one needs a model for most serious wide-angle shots. I solve the "Whale Shark cruising by" problem by also carrying a Sanyo HD-2000 video/still rig.