Indeed, any feat you're expected to take, from Toughness to Weapon Expertise, devalues the feat system. Feats were designed to be character options - ways for you to define your character. As soon as certain feats become something you're expected to take, they're no longer options.
Sure you have the option of not taking them, but you're expected to, so it's a rhetorical choice.
I what campaigns I've run or played in, Toughness hasn't been so much a necessity, so I'm fine with that. It's good for making a character feel tougher, but if you want a character that doesn't feel all that tough, not taking the feat isn't a death sentence.
The Expertise feats, however, immediately became so mandatory among my gaming groups and fellow players that they revised their builds or retrained as soon as they leveled up, making it obvious how these feats were no-brainers. I've subsequently given players a +1 bonus to all attacks at levels 5, 15, and 25 and removed the Expertise feats, freeing up that feat slot for the players again.
Anyway, what I wanted to say, I guess, is that implementing "math fixes" like this should not be at the cost of the optional elements of character design. If it's a general flaw in the math of the game, make a general errata that affects all characters regardless of character design or concept, not something you need to be aware of as a player and then pick the right feat to compensate.