Yes, you can swap an ISIS BB for an integrated/external style, such as MegaExo, or Shimano's Hollowtech. Just make sure to get the threading right, either English or Italian. If you get an integrated/external style crankset, you don't have to worry about chainline because the axle is built into the right side of the crank, and is already the correct length. If you stay with a cartridge style BB and crank, like
ISIS or a square taper (don't discount them, there are some nice options for those as well) you will need to get a BB with the proper spindle length to have a proper chainline. It isn't too hard to figure out since most cranks list what length BB they need. Personally, I would go with that Shimano RC700. It shifts better than the FSA due to its better engineered chainrings and I think it looks better, but that is just me.