The good ending was one of the most awesome good-guy moments in all of gaming. Watching the girls come to grab your hand as you lay in your death-bed was the most good guy awesomeness I've gotten in video games since saving Christmas in EBA.
Of course Fontaine was weak. System Shock 2's final bosses were equally unimpressive.
Really, when you get right down to it though... wasn't that the absolute most ridiculous, dumbest, most completely absurd plan known to mankind? I almost didn't believe the "Would you kindly" bit because it was so moronic. You want to kill Ryan, so the only way you can do it is to clone his child, accelerate his growth, send him BACK TO THE SURFACE, have him CRASH AN AIRPLANE AT PRECISELY THE RIGHT TIME (He'd be lucky to survive!), find his way through Rapture, marvel at the fake death of your fake family, and kill Ryan, even though you could have just said "Would you kindly kill Ryan?," even though RYAN WAS IN A

ING UNDERSEA TIN CAN THAT COULD HAVE BEEN PENETRATED IN ANY THOUSAND LESS STUPID WAYS?!
In the end, a really, really stupid story told really, really well. A worthy sequel to Bioshock, but the less time spent actually thinking about the sequence of events in the plot vis-a-vis Fontaine and Ryan, the better. Which is probably why the endings were FMVs completely to that central struggle.