I haven't used ISBoxer yet but the only advantage over keyclone that I see is near instant swapping of the windows. With Keyclones latest release it has reduced the time to swap windows but it still takes 2-3 seconds. The videos of ISBoxer I have seen the swapping happens almost instantly.

I am wondering how a FTL system would be setup with all the toons you have.

3 choices of tank * 3 choices of healer * ~10 choices of dps = ~60 combinations

Not being a user of FTL is this the type of assist macro he is going to need to along the lines of

/assist [mod:shift,nomod:alt,nomod:ctrl,target=Toon1][nomod:shift,nomod:alt,mod:ctrl,target=Toon2][mod:shift,nomod:alt,nomod:ctrl,target=Toon3][nomod:shift,nomod:alt,mod:ctrl,target=Toon4][mod:shift,nomod:alt,nomod:ctrl,target=Toon5][nomod:shift,nomod:alt,mod:ctrl,target=Toon6][mod:shift,nomod:alt,nomod:ctrl,target=Toon7][nomod:shift,nomod:alt,mod:ctrl,target=Toon8][mod:shift,nomod:alt,nomod:ctrl,target=Toon9][nomod:shift,nomod:alt,mod:ctrl,target=Toon10][mod:shift,nomod:alt,nomod:ctrl,target=Toon11][nomod:shift,nomod:alt,mod:ctrl,target=Toon12][mod:shift,nomod:alt,nomod:ctrl,target=Toon13][nomod:shift,nomod:alt,mod:ctrl,target=Toon14][mod:shift,nomod:alt,nomod:ctrl,target=Toon15][nomod:shift,nomod:alt,mod:ctrl,target=Toon16]

Granted you could probably cut this down to 3 toons (the tanks). I think once you wrap your head around how FTL is supposed to work it isn't that hard to implement. I know at least personally I would like to figure out what the macros are doing not just have some tool generate everything for me. If you figure it out yourself (or with help from others who have already done it) then when something breaks you can fix it.

One thing you might want to look into is using the a system designed around party targets. I could see a system of macros where everythign is based off of target=party_ . If you always had your tank as leader than each dps could just assist party1 that way it would work no matter what tank you had at the moment.

Short Version: Your Software is fine tweak your Macros to what you want to do.