We stay at the Poly since that's our home resort. I've found it faster to walk to the TTC and take the Ferry boat over to MK the last 2 times we went.
For Epcot, we walk to the TTC and sometimes the monorail is down and then we catch the bus. Other times the monorail is running just fine to Epcot.
I split our stay between the Poly/BLT last time and planned our days so when we were at BLT those were the days we went to MK since we could walk. That worked well.
I guess we've been lucky that it hasn't affected us too much. Now that I've written that I just jinxed my next trip which is a split stay between Boulder Ridge Villas and the Poly DVC.