Every offense of every kind will have open guys that don't get thrown to. The progression system basically guarantees that and it is the only viable system. You can't have a QB trying to check 5 different receivers before throwing on every play. He'll be sacked 10-15 times a game.
Teams don't really "sit" on those two guys. They play zone 85% of the time. If those guys run into a zone the defender with responsibility for that zone covers them. Guys responsible for other zones don't. If they did, it wouldn't be zone coverage and the integrity of the coverage would break down. That's why even though teams know the ball is likely going to Hill and Waddle they can't/don't really stop it. Even in those bad games late in the year they were regularly open, but passes fell incomplete due to bad throws and drops.
The problem with Miami's progression is TH/Waddle were almost always 1-2 in progression (slight exaggeration). Mcd knew that as well, but still didn't change progression. It's one thing to not have time to throw to an open guy, but completely different to know a guy is open but not target him.
I know you'll likely disagree and some may flame me for this. I know what the stats say about Miami facing zone, but, as the season progressed, it was COMMON to see TH with 2-3 defenders within 5 yds. Sometimes quadruple coverage. AND waddle double covered. TT had so little time he threw jump balls into triple coverage. But STILL they were 1-2 in progression. I can't see that as a standard NFL zone.
One game in particular the talking heads would show replays and point out defenders sitting in the timing windows.
I agree teams didn't play man often and I don't blame them. But it's hard to have a receiver triple covered in zone.