The match making is designed to simply look at GP (up to a set number of toons per division), which means pay to play will likely have an advantage - more likely they will have highly geared meta teams. But I've had more close matches under the new matching scheme than the previous total GP failure, though still get the odd one I have no chance of winning (I have no DR or Malak, so when my opponent does I find I'm screwed).
But at the end of the day, you have to give the pay to win players an advantage. Why else would they spend money on the game? It keeps the game going so the rest of us get to play for free/cheap. If you can learn to accept that, it is a lot less stressful.