The complexity of setting up an FTL system is greatly reduced if you have a /click macro that takes care of the targeting. If that's the case, then your other macros are all very small and simple (simply referencing the click button and then casting the spell).

As far as Fur's comments of what happens when the main toon dies, that is exactly the FTL's strength: flexibility. It doesn't matter which of my 5 windows I'm in, if that's where I hit the keystroke from then all others treat that toon as the current master without me having to do a thing.

I agree that the FTL system is more complicated to set-up than the focus-based system. Other than that extra complication, the FTL system is superior in every way since it has the flexibility to do everything the focus system can, but also has other functionality. In my opinion, it's analogous to HKN and Keyclone. Keyclone is reportedly more simple to set-up, but I know HKN has more functionality once you get past the initial stage. Does that mean every user should use HKN or an FTL system? Absolutely not. All it means is that if you want to have the most "powerful" system, then those are your best options. If you are most interested in initial set-up, then perhaps Keyclone and focus-based is the best option.