Not sure asking the question of "which manufacturer has more of the engines you're interested in" is all that helpful, actually. Both Lionel and MTH make or have made practically every conceivable engine you could want. For simplicity of setting the system up, Legacy is significantly easier to set up, and less problematic in operation, as others have said. The point made above is a good one that all the other manufacturers' engines such as 3rd Rail and Atlas O, as well as K-Line and Weaver (no longer in business but a lot of these engines are around), use Lionel electronics, so Legacy would be most compatable with these if you ever decide to acquire some of those engines.
I'd also seriously consider Landsteiner's comment about going with Lionel LionChief Plus engines as a starting point. If a person is new to the hobby and doesn't want to spend a fortune, this is a smart way to go, IMHO. If you later decide to get into Legacy, the LionChief engines are compatable. They will run on MTH systems, also. If choosing something in the LionChief series, keep in mind that the LionChief Plus engines are a significant improvement over the regular LionChief engines. They have a cruise control system built in, which adds a lot to the operation of the engines, so I'd suggest looking at these Plus engines.