No doubt about it. My company used to allow as much manual flying as you liked, with FD's off Man Thrust, raw data etc. But we were bought by a bigger neighbour and now we have to follow their very inflexible SOPs which as you probably guess, prevents us from turning the FDs off (except for visual approaches which are few and far between on our network) and only allows manual flying if the weatehr is good at a familiar airfiled. On the face of it, it's safer. But it doesn't take into account the degradation of our skills.
On the last three days of our own SOPs, I flew 8 sectors with the same pilot. We agreed that all our briefings should be "Standard" and all approaches flown manual with raw data as it was the last chance we would have. We had a great time and at the end of it, we both saw our skills improve as we got practised. And there was no degragation of the safety margins as the weather was OK and we carefully monitored each other.
And now we have been under the new system for 6 months. I'm sure my skills have degraded.
The FAA have just regulated against lower hour pilots holding ATPLs (not quite the right response IMHO) and Airbus have issued a statement saying pilot's skills are diminishing. The industry recognises the problem but the airlines don't seem to want to listen.