I like bigs on the court for everything you describe as their weakness.
1) 5 out is a bad offense because it parks two players in the corner where they can't rebound and where they are as far from defending their own basket as they can possibly be and still be on the court. A long rebound or a turnover turns into a layup the other direction. A 5 out also shrinks the gaps between defenders, enabling the next defender to guard the gap and still guard his man, which makes penetration more difficult. Finally, there is no rebounding in a 5 out.
2) against man defenses, run P&R with the center, or run our normal top of the key screen sets but with one of the bigs setting an off ball screen for the other big, who is then coming downhill at the basket, one dribble from a dunk or layup.
3) Against zone, high/low the two of them, with Reed above the free throw line and Johnson flashing short corner to short corner. Centers defending in a zone HATE high low action because any basket makes it look like they screwed up, and Johnson on the weak block (where he will usually end up) will force the wing defender to collapse, leaving Ball or Mahaney wide open on the wing for a kick out.
4) I don't want Ross or Diarra taking a lot of 3's anyway, so pulling Ross in particular off the court just means more 3's for the other shooters like Ball, Mahaney and Stewart.
5) If they double Reed on the block with Samson's man, Reed throws it up at the rim and Johnson dunks it. With the inside players most teams have, Reed is going to spend a lot of time on the free throw line if he posts up.
6) Reed and Johnson have the 4th and 1st highest ORtg on the team, and both are way ahead of any other rotation player on DRtg. Stewart is higher than Reed's ORtg by .2, but Stewart has a 110.7 DRtg, which is the analytics equivalent of saying an 85 year old woman with a walker could take him to the hole anytime she wanted.
7) Reed's and Johnson's shooting percentages of 65.6% and 79.3% from 2 mean that their 2 point attempts have a higher expected value than every player other than Ball's 3 point attempts, and that is before addressing the higher number of fouls inside players draw.
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Teams figured out how to play with two bigs 40 years ago. Celtics won a bunch of championships with McHale and Parish, and the Knicks got close a couple of times with Ewing and Oakley and a bunch of guards that couldn't throw a basketball into the ocean. The Bucks won it 4 years ago with a 4 that is so bad from behind the arc that the other team literally runs away from him when he sets up for a 3 just so he will shoot it. I think we can tweak our sets to get two of our best players on the court more.