I have about 100 hours in a 2006 Encore.... what a pleasure to fly. BUT its still the same small jet cabin .....

Personally if comfort is the main concern.. and access to a lav... go with the excel.

My last company had a customer who had gotten use to the excel we had.... the owner moved the aircraft to the west coast and the customer started flying our encore most everywhere. their main complaint was NO real lav and lack of near stand up capability.