Again, personal preference to me. The disadvantage to the interlock is that it does make you choose one source or the other for everything, period. Of course you don't have to have all the circuits on, but then in some houses that have multiple sub panels in differne threads, this is more of a hassle.
I'll have to re read but the one I linked based on a quick view of how its wired, allows you to leave other circuits wired to the main service and turned on, because the transfer panel is wired in after the main panels circuit breakers, and there fore chooses a source for the circuit after the main panel circuit breaker for that circuit, and not a source for the actual panel.
Anyway you look at it, the automatic transfer switch is the best way to go. I've worked on them and as soon as the juice comes back the switch flips and you are back on the grid. We used big diesel generators in our plant and never had a problem. With the transfer switches, I mean. The generators were old and a pain, but that's another story.