It's worth distinguishing two different questions here. First, are there many other players better than their Limerick counterparts? Second, are there many other players who would fit better into the current Limerick team, i.e., improve it while the rest of the team remains the same?
For instance, I think Conor Whelan is a better player than Flanagan, but Flanagan plays a crucial role for Limerick's attack, and both he and his team-mates know what his job is and how he will go about doing it. So even though Whelan is imo a better player, bringing him in might weaken the team overall.
Or take John Conlon - it's doubtful imo that he would improve Limerick, but I reckon he fits the current Clare team better than Hannon would.
In terms of players who might be better than their Limerick counterparts, in addition to Whelan and Kelly I think you could make a case for Lawlor or Daithi Burke at FB, Fitzgerald at midfield, Eoin Cody and perhaps Dessie Hutchinson or Rory O'Connor in the full-forward line. I'm not for a moment saying any of these are clearly better, but in each case there's at least an argument to be had.