Yes, I completely understand! BWI and Poly are two of our family's favorite resorts. So our solution for longer stays is to start at Poly for a couple nights and then transfer to BWI. We were originally booked at Poly for the Princess Half Marathon weekend and then changed our reservation to BWI CL based on all the uncertainty of Poly construction. Next year, depending on Poly construction, we'll either stay at BWI or do a Poly/BWI split again.
Of course, Poly and BWI are quite different. Overall, I prefer BWI for a number of reasons. We love Epcot and we have dinner ADRs in or around Epcot every night. It's so easy to get to/fro dinner at the end of a busy day when staying at BWI - just can't beat strolling back to our room. We also love the ability to walk or boat to DHS. I love CL at BWI, love a room with a boardwalk view (my favorite in all of WDW so far!) and like the room decor.
So the ability to walk/boat to Epcot and DHS are key factors for us. And the bus to MK is fine. In principle, I do enjoy the quick monorail ride from Poly to MK in the morning and the boat on the way back to the resort. Although in recent years, we've found that monorail resorts are not always the most convenient for us. For example, one morning while staying at CR, we took the monorail instead of walking "for fun." Monorail was not working properly and the trip took 45 minutes - not kidding - causing us to miss rope drop. Last year, when staying at Poly, it took us 1.5 hours to get back to our room from MK at the end of the night. And that was during value season. It was just mobbed - monorail lines were huge and the boats were just as bad. We watched numerous Epcot area resort buses pull up, load and depart. My husband was lamenting the fact that we had not yet transferred to BWI! These are just a couple examples of several issues we've had with monorail service that prompt us to choose Epcot resorts more frequently.
As for counter service, we solve our breakfast issues by staying CL, which we really enjoy. And we usually have ADRs for lunch and dinner. But when we need CS, Boardwalk Bakery is really convenient, or if we have a few minutes, we hop into World Showcase and get sandwiches from Les Halles. One of the things we like about BWI is that is doesn't have a food court or crowded CS location. I love Poly, and Captain Cook's is high on the list of resort CS, but it's still crowded and I definitely prefer a quick stop at Boardwalk Bakery or the short walk over to France.