I've now worked in both a 141 school and a part 61 shop. I like 141 better, but that's mostly for administrative reasons... I also understand that this gets to be like "Coke vs Pepsi," "Chevy vs Ford," or "Boeing vs Airbus" real fast.
Getting final stage checks for my students in the 141 school was much easier than scheduling a DPE at a 61 school. Career students can also jump straight to an instrument program immediately following their private and can enroll in the commercial course not too much beyond the instrument. I think the 100-200 hours immediately following the private pilot rating are the most dangerous and most formative of a pilot's career...141 programs can make those hours be in a training program vice the pilot roaming the country VFR.
My issue with part 61 is that I think it allows bad instruction to continue. We all have had great instructors and I think the best are usually under part 61 operations, but we've all probably had poor instruction at some point as well. The FAA doesn't make CFI check-ride pass rates public, so there's little data to make a student decide on a CFI besides simply word of mouth. A good 141 school tracks student progress. They should be comparing all the students among each other as well as each CFI's performance. If student X didn't solo until the 30 hour point, then maybe a flight with the Chief Pilot is warranted. If all of CFI Y's students are soloing at the 30 hour point, then maybe the issue isn't the students...
As for flexibility, I found I could make a 141 program bend, as long as I accomplished all the lessons in the syllabus by the end. To me, the biggest downside to a 141 certificate these days is having the FSDO aircraft maintenance inspector climb over a school's aircraft. I've seen the maintenance inspector generate $10K worth of work for a school in a single afternoon. That kind of financial risk is a turn off to most places...
