I've used both starting with the focus method. /assist focus is no faster than doing an /assist <toonname>

The only real difference is the macros. Focus is very straight forward and can be set up and running rather quickly. FTL takes a little more work to set up, but can be just as easy to configure once you understand it. One big advantage for me using the FTL is that I have two main macros on all 10 of my toons (I run both 5 shammys and 5 druids). One for following, and one for assisting. The assist macro is referenced from every command that needs to be targeted, and the advantage is that if I decide to interchange some of the toons (ie. 3 shammys, 2 druids, etc), it's a simple as logging into them, and all the macros already perform the correct assist / follow. The real challenge here is deciding how each keys will be mapped (ie. my flameshock and insect swarm fire together, starfire and chainlighting, etc).

Someone on here posted a link to SuperDuperMacro or something like that that allows huge macros, so both my assist and follow macros are using that. The cool part is that if I decide to roll up another new team, I simply add their names to both of the macros and the rest of the foundation is already set so that the team can be interchanged.

The real question you need to answer is that if you care if you can control all aspects of your toons regardless of which window happens to be in focus at the time. In pvp, this can be a life saver as your lead toon is usually easily identified and focused down rather quickly, and when this happens, you'll lose your other toons if you have no way to attack or defend.

With FTL, I find myself constantly switching leaders between arenas, BGs and WG, so when your opponents see you, they don't formulate a quick strategy to focus your leader down for a quick win, and realize that there really is no leader.