A lot of the issue now with Doyle is a secondary impact of teams adjusting to Thomas' pace. Word about Thomas' speed seems to have got around the division now and recently teams have started playing deeper to negate it. This stretches the area that the midfield need to cover which makes his anchor role ineffective and exposes some of his own weaknesses with pace and agility - if he needs to cover more ground he's ended up chasing a lot of shadows.
Ultimately we have to get more bodies in midfield in that circumstance and I think there's a few realistic plan B options without making sweeping changes:
1) Play a high line ourselves to close the gap in midfield (we did it very well at the start of the 2H against Peterborough, both Doyle and the fullbacks starting position was on halfway) but there's higher risk defensively by leaving a big gap in behind our team, and without Willis our back 4 is very pedestrian - none of Brown, Grimmer, Davies, Hyam or Doyle are quick and Burge has been historically poor at coming off his line.
2) Change to a 4-5-1 to get an extra body in midfield - Chaplin has been trying to do it but for me we need a proper midfielder in there to go to a true 4-5-1. It might seem like a negative change to lose a striker but I'd rather have a ball winner like Ogogo or Kelly to link play and let Bayliss play higher. Thomas, Bayliss, Hiwula, JCH should be enough attacking threat with a solid midfield behind them and I think this is a viable option to change for the 2nd half of games when using the subs, rather than just changing personnel in the 4-4-2.
3) Get the fullbacks playing higher up the pitch. Leave Doyle in his anchor role, get the fullbacks higher up the pitch, tuck the wide players inside a bit to bulk out the midfield and give us 2 extra options for shorter forward passes This option I see as an interim change e.g. something to try for 10 minutes to drag the opposition out of their own box as they try to match up with our change.
Just some thoughts anyway. As teams are adjusting to our strengths it is exposing unexpected weaknesses and I'd like to see a better plan B in those circumstances.