If you are looking at "cheaper" used boats, then IMHO an outboard will likely be nothing but trouble and expense. I've never had an i/o, but it seems to me that they would have the advantage in longevity, being 4-stroke and basically a car engine. Two stroke outboard engines don't have anywhere near the life expectancy of a car engine, no matter how well you take care of them.
If you buy new, there are a bunch of 4-stroke outboards that start to blur the line a little. They are much quieter, more fuel efficient, and probably longer-lived than carburated 2-stroke outboards of the past. They are big $ though.
As I said, I've never had an i/o but if I were looking for a used ski-boat, say 10 years old, I'd have to vote against the outboard, leaving but one choice, the i/o.
As with anything, the way in which it was taken care of is important. With boat engines, it is paramount. Regardless of which engine type you are looking at, I'd talk to the seller and ask them:
How often they changed the water impeller (every 3 years, minimum, or the motor may run hot, reducing it's life)
How often they changed the lower unit oil (every year, also need to check it for water intrusion, forming a milky color)
Whether they run a water-seperating filter on the fuel line (not an absolute must, but great peace of mind that the motor hasn't had water in it).
Does the power trim and tilt work (if so equipped, and I wouldn't have one without it).
Is there fresh grease at all pivot points and on the zerks (or at least wiped off after lubing).
If they look at you blankly when you ask these questions, run away unless they have maintanence records from an outboard shop.
And don't forget to look the boat over too. There's a lot of things that can be wrong with a 10 year old boat, not the least of which might be a cracked transom or a patched hole in the bottom of the boat.