I think the ideal personnel for that play would've been:
Flowers; Butler; Simon or Clayborne or Davis (as pass rushers)
D. McCourty; Harmon; Gilmore; Chung; J. Jones; JC Jackson; J. McCourty; Melifonwu or Ebner
Get your most athletic, best tackling players on the field. Those types of plays (final play situations where a short throw followed by laterals and RAC will be involved) should be treated like a special teams situation, in my opinion.
Perhaps you could consider trying to get a LB out there like Van Noy, or another special teams specialist like Grigsby, Humber, McClellan, or King.
These type of plays are a prime example of an in-game situation that I would expect Belichick to be ahead-of-the-curve and intuitive about; understanding that this won't be a long pass, but rather, a short pass followed by a lot of running, and thus, should be treated as a special teams/return situation. It makes me wonder if Belichick is perhaps losing his cunning edge (this seems extremely unlikely to me), or if he's giving a lot of responsibility to individuals (Flores comes to mind) who aren't as innovative and forward-thinking as himself.
Assuming Belichick really is delegating a lot of responsibility to Flores, I would be genuinely curious to see Belichick himself having a more involved role, essentially serving as the defensive coordinator in the future; it's been awhile since we've seen that. He could let McDaniels handle the offense, while Belichick focuses solely on the defense. I'd be curious to see if we notice a difference. Perhaps next season?