They tried to save Flintoff from himself a number of different ways and they did try to limit his overs (it helped when they had the likes of Simon Jones or Harmison in his pomp, to pick up the slack) but they never really managed it because of a) ego (he was also told to change the angle of his plant foot at the crease as it was going to knacker his ankle - he refused as “this is the way I bowl and it’s successful” and sure enough his ankle did for him) - and b) they gave him the captaincy and he bowled himself into the ground (think there’s one game against Sri Lanka where he bowled 50 odd overs in an innings due to his own decisions).
Flintoff should probably have been used like Stokes currently is. The guy you turn to when you need a partnership breaker or a bit of inspiration. He ultimately probably bowled too much and it shortened his career.
On Stokes taking the new ball: If Anderson or Broad doesn’t play, good chance Archer is in the side and will open the bowling. If neither of them play, good chance someone like Wood or Stone is in the side as well as Archer, both of whom tip the radar gun at 90 mph. I think you’d probably want to give them the new ball due to their pace, so they get chance of using it whilst it is hard. Also, the reason that Anderson and Hoggard opened the bowling is swing, so even if none of the non-Archer fastest bowlers are in the team (England will, in the fullness of time, always play Archer if fit, I suspect), if someone like Woakes is in the team, you’d still want him to have first use to try and get the natural swing from a new ball.
Stokes is also one of England’s men in the slip corden - if you have him bowl with the new ball, when edges are perhaps more likely, you’re taking him out of that area. I suspect that they may well want to leave Stokes as the 4th seamer to be honest - as with Flintoff, it may help to restrict his overs too (if the first three seamers are doing well, you keep them in rotation as the Aussies do with their quicks) and thus save him from injury. His batting is now too important - he’s arguably England’s best bat now, especially given Root’s extended run of form.
Of course, problems then arise because Wood is made of glass and they keep talking about how Archer should have his overs limited to shock bursts to make the most of his pace…there are unlikely to be easy answers.
Arguably the best things about Broad and Anderson are their ability to bowl for long spells without going for a lot of runs. Judging by what is coming through (and the inability to find a spinner to bowl like Swann in a similar holding role from one end for ages), this is going to be the core hole in England’s bowling line up when one or the other of them retires.