<G11>
f2.8 max
5X zoom not much use underwater but useful above
Larger size, smaller flip out LCD, will not fit in pocket
Wet lens challenged--double bummer
Perhaps better macro
Small and nearly useless optical vf
Has a hotshoe
No lens ring control--bummer
Housings by Ikelite, Canon, FIX, Patima, others?
<S90>
Faster f2.0 lens (twice as fast)
4X zoom better interfaces with wet lenses
Smaller size, larger LCD, fits in pocket
Depending on housing choice works with various wet lenses-- triple yippee

No optical vf---bummer
No hotshoe
Intuitive multi-function lens ring control---yipppeeeeeeee
Housings by Ikelite, Canon, FIX, possibly others in future
Which of the two is better depends upon what you value.
The G11 and S90 use the exact same sensor and processing engine, the S90 has a faster lens and direct control of both shutter speed and f stop via rear and front lens control ring. Neither have HD video as they are intended for serious amateur photogs and the emphasis is on picture taking. The G11 has weird flip finder but some may enjoy that feature for candids.
The S90 has essentially rave reviews across the board for it's intuitive interface, low noise and fast f2.0 lens. You can get the same shot at 1/125 the G11 must drop to 1/60 or at ISO100 instead of ISO200 or shoot at ISO400 instead of ISO800 with the same settings, speed might matter to some people. The camera is very small and pocket-able and at least one of the housings, the FIX90, is actually smaller than the G11 sans housing in some dimensions.
On the other hand, the G11 is the latest successor to a long line of Canon G series loved and enjoyed by many. Probably a better SLR stand-in if you are a one camera person topside and bottom side. The FIX housing does have a wide angle option and the Patima supposedly does and the Ikelite at least has a corrector port available so all is not lost there either.
Me, I valued, little, fast and wet lens options and direct interface. Next year, who knows. G12 with DX sensor?
N