Last year we did a few counter service breakfasts at Pop Century. They had very good options! The only other CS breakfasts that I know of would be Tusker House in AK, also quite good, but definitely not as many options as your hotel food court will offer; ABC Commissary in Studios, and either Sunshine Seasons or Electric Umbrella in Epcot (I think they've switched from EU to SS??? Not sure.) I know you can also use CS to get a couple of pastries and a drink at the Boulangerie in Epcot, and you can get the special at Kringla, but I'm pretty sure that is more of a lunch meal, they may have the two pastries deal too.
Honestly, the best CS breakfast you'll find will be at the hotel if you want a big breakfast and not just a pastry.