I think you are underestimating the amount of con saves that will be needed. Concentration checks, poison, undead, most of the necromancy school of magic and much of the transmutation school will be con checks. In fact a lot of the really bad stuff
Say we have a PC that wants to boost CON as his second ability score boost and he starts out at level 1 with an even CON score, and is a class like Cleric or Wizard that gets it at 4, 8, 12, 16, and 19. Compare that to the same PC that takes Tough at level 4, but still boosts his CON. For seven levels, he has a better +1 CON mod. For 17 levels, he has much better hit points. Granted, he's also lowering his main ability score by 1 for 7 levels as well, but that's the price for more hit points. Hit point damage can occur nearly every encounter.
So, level, CON save bonus without Tough, extra hit points without Tough, CON save bonus with Tough, extra hit points with Tough 2/level
01 +2 0 +2 0
02 +2 0 +2 0
03 +2 0 +2 0
04 +2 0 +2 8
05 +2 0 +2 10
06 +2 0 +2 12
07 +2 0 +2 14
08 +3 8 +2 16
09 +3 9 +2 18
10 +3 10 +2 20
11 +3 11 +2 22
12 +3 12 +3 36
13 +3 13 +3 39
14 +3 14 +3 42
15 +3 15 +3 45
16 +4 32 2 +3 48
17 +4 2 34 +3 51
18 +4 2 36 +3 72
19 +4 2 38 +4 76
20 +4 2 40 +4 80
This PC jumps up 8 hit points (over everything else) at level 4, 14 more at level 12, and 19 more at level 18. The bold levels are the one where not taking the feat Tough gives a CON save bonus of +1.
Going from 17 hit points at level 3 for a CON 12 wizard to 30 hits points at level 4 nearly doubles his hit points in one level. This is fairly significant.
He can get hit for hit points damage nearly every encounter, but he gets hit for CON saves once in a while. In the Starter Set, there appears to be 5 monsters out of 22 that require CON saves (but not necessarily every attack). So rough rule of thumb, that's 5% of the hits that it will matter (+1 more on CON save), for 7 levels out of 20, for 5 out of 22 attacks or 0.04% of the time.
1 hit out of every 2500, it matters.
The CON save issue seems like a quibble to me.