We were just there - 10 nights at Fort Wilderness - and we loved the security changes. As we exited the boat, they were there to check us - super fast and easy. No more long lines.
The only thing that seems strange to me - when leaving the Contemporary for monorail, we were checked, then when we got to Epcot, checked again.. They haven't figured out a way (and probably won't) to keep monorail resort guests separate for that park. Not a real 'biggie' though - just double checked to get to Epcot from a monorail resort.