Thorn bird: Standards have probably changed but not improved. There's areas where modern students are pretty good: procedures, complex aircraft systems, navigation & GPS, radio calls & CTA procedures (ok, radio calls when under stress can be crap, but nothing new there). But that's the nature of modern training - emphasis on checklists (well, do-lists) and procedures. Lots of emphasis on getting easily monitored stuff accurate (eg. cruising alts).
But other stuff seems to be missing - navigation can be pretty ordinary, because on solo navs they are following the pink GPS line; traffic and situational awareness the same, for the same reason. And handling abnormal attitudes can be lacking. It's almost unheard of for PPL/CPL students to have done more than wing-drops before gaining the license (and if they have, it's likely by rote), and I've seen plenty of students who didn't cope when exposed to something more than S&L or planned "steep" (45deg) turns. They are the ones who have the potential to move onto being AF447 crew
And to actually answer your question - I think Part 61 probably has had a negative effect overall. Because there are LOTS more boxes ("competencies") to tick, there is less room to adjust the students' training, and more emphasis on plodding through to meet prescribed standards.