I don't have time to read the whole thread (at work), so apologies if this has already been stated.
I think the sensor system you guys have in place is pretty nice. Makes sensors more important, and makes it easy to understand. I don't think newbs will have too big of a problem...worst case, they don't know why the IFFs are gone, they ask, they get an answer, now they know.
I don't think deployable sensors will really bring anything other than a complication. Adding deployable sensors will require a change in the single-sensor idea, it'd probably have to follow the T2-style sensor system so that it's not too complicated for a newb.
As far as the flag IFF/waypoint goes, I like the idea of having it by default you get a waypoint for the flag, kinda like a homing beacon. Then, if the sensor's up, you also get the IFF (I'm assuming this is what you're [KP] talking about) if you have LOS to the flag carrier/stand.
So, assuming I'm a capper going for the flag, if my sensor is up, I know exactly where the flag is (IFF + waypoint), I just go for it. If the sensor's down, I know the position of the flag on the CC (waypoint), but there's nothing in my LOS to show me where it is. Not detrimental to capping, but it does make it a tad more difficult.
Now, if I'm going after the enemy capper who has our flag, and my sensor is up, I know where they're at (waypoint), and which enemy has the flag (IFF). If the sensor's down, I know where they're at (waypoint), but not which enemy has the flag...so if there's a group of enemies sitting around where the flag is, I gotta pay a little more attention.