The brake controller will not be in the way of plugging in your programmer.
The brake controller plug in is above and behind the OBD II plug in. You can route the wires for the brake controller to the side to avoid being near the OBD port.
As far as controllers... The Tekonsha Prodigy is the #1 selling brake controller in the country by far out selling it's nearest competitor by at least 5 times. That being said it is not Tekonsha's best or top of the line controller. It is just the best features per dollar available. The Tekonsha P3 does everything the Prodigy but additionally lets you control the display color and error codes are in plain English.
The more you tow the cheaper the controller you can get away with as you understand their limitations and control functions. The absolute minimum controller you should look at is timer based controls like the Draw-Tite Activator II or Tekonsha Pilot. Inertia is usually a step up but controllers like the Tekonsha Voyager I see as a step down because they are very difficult to set accurately. Never really liked the Primus.. can't really articulate why.
Like a million threads like this already in this forum, most agree on the Tekonsha Prodigy as the go to controller.. second if you must spend more $$ then step up to a P3.
Last edited by Colorado Osprey; 02-22-2012 at 08:51 AM.