you are missing the whole point, formation subs are not for guys to take a 'breather'
alot of guys in the nfl now esp on defense and esp in the front 7 are situation specific players, such as run stopping NTs, pass rushing DEs, coverage LBs etc etc
in your base 4-3 you are going to be run oriented, with bigger linemen and LBs with higher blockshed and str
in passing situations, nickel/dime, you may plug in smaller but faster linemen to rush the qb and/or drop into coverage. you also may play different LBs who may be faster with better coverage skills
i know the rams for an example use 4 DEs in nickel and dime packages, the falcons switch out LBs in nickel and dime (just 2 of many many examples)
most big run stopping DTs only play in run situations in base defense
you also do not want to get stuck in your base package (with your big lineman) in 2minute drills
formation subs effectively knock out 2 birds with 1 stone, you get the chance to put the best guys on the field for each situation and you are limiting snaps for certain players so that they may have more left in the tank at the end of games
on offense WRs are rarely situational, instead their snaps are simply monitored and they often come out a play or too after a big run to catch their breath
auto subs work good for offense for the most part as you want your best guys on the field and 3DRB has its own depth chart spot
formation subs work best for the defensive side of the ball
i also usually put in my 3DRB in on all shotgun plays
and having a receiving TE and a blocking TE both can come in handy in jumbo formations vs regular formations
would be nice to decide who plays special teams aswell...
honestly it was a great feature that made no sense to remove...
unlike CFM coaching schemes now (which have no real impact ingame)