edit: just read KP's thing about LOS, so ignore the LOS stuff here
If the sensor is off, it doesn't matter that you can't see the enemy IFF, because you will still see your friendly IFF. A way to fix this, is to make friendly IFFs go away when the sensors are down. However, this would slow down the game because instead of going right to the action, you are trying to figure out who's friendly. So we want friendly IFFs on all the time. I don't really see a point of a sensor in this case. You can tell who is the enemy by who does not have an icon over their head. So I would have friendly and enemy IFFs on all the time (well, obviously you wouldn't see them through buildings, and you wouldn't see them if they aren't in your LOS).
As for the radar, I think having enemy AND friendly icons turn off when the sensor is down would be interesting. It would give a greater incentive to keep the sensor up. You can't coordinate caps very well if you can't see the positions of your other teammates. The slow down arguement in the first paragraph might apply here, but it might be something to try.
For the flag IFF: I can't stand having an icon over the flag all the time. As a compromise, I think the flag IFF should only be on the screen if the sensor is up. However, the icon will only show up if the enemy is in your LOS. The flag will show up on the radar if the sensor is up, it won't show up if the sensor is down. I know it seems kind of silly to have it show up on the radar and not show up when the enemy isn't in your LOS, but I also think it is silly to have an flag icon hovering in the
background when you are no where near the flag.
In CTF, there's a problem to adding another objective. You already have flags, generators, and turrets to take care of. With the smaller player sizes in the game (lets say 8-10 per team), can a team really defend everything in the base? Flag indicators are a huge part of the game, so are the generators, and of course the flag. How can teams possibly defend everything? In T1, it really didn't matter since most teams didn't use sensors effectively. So you only had to worry about the gens and flag. I don't really know how a team can defend everything with smaller teams.