Re: Why are ski / wakeboard boats inboards?
The main issue, as mentioned above, is that ski/wakeboard boats are designed with their respective sports in mind. It is almost impossible to get an I/O or even O/B to give the holeshot and minimal wake of a tournament ski boat. The other advantage of ski/wakeboard boats over I/Os is tracking. When a 200lbs slalom skier is pulling hard through a course, the Inboard boats will track much better and eliminate most of the tracking issues. Try it with an I/O of equal size and you will have the stern of that boat being pulled everywhere.
As far as wakeboard boats, the V-drive config is a safety thing, as many people are in/out of the water often, and wake-surfing is done a few feet off of the swim platform, so it'd be dangerous with an I/O. The lack of equipment in the water makes the wake very clean and smooth, unlike the I/O's which create a lot of turbulence.
Drawbacks - trim. The inability of ski/wake boats to trim causes significantly more fuel usage at any speed over where an I/O would normally plane out. Also, tournament ski boats tend to have a very low freeboard, so passengers will typically get wet when there is any chop/wake on the water as they don't have the ability to trim the bow up.
Side note: the "fat sacs" etc can be had on any boat, and many manufacturers of I/O's offer the "perfect pass speed control", and ballast systems just like the ski/wake boats do. The only reason the ski/boats cost so much more than I/Os is because of production numbers. The economies of scale aren't there, but the engines are identical to what Mercruiser uses.