I think traits are a poor vehicle for this kind of change
From the outset, I want to say that this is a massive change compared to most traits. Traits are tiny things, +1 or +2 here, −1 or −2 there, and that’s what they’re supposed to be. Fitting such a large change into the same “slot” is extremely awkward, and really quite dubious.
Balance is not the only consideration
Having a large benefit with a large downside has different effects on the game than a small downside with a small benefit, even if both “balance.” It can make things more “swingy,” it amplifies the significance of min-maxing, and introduces character “skew,” where a character is too good in some areas and too poor in others. Obviously, all characters should have strengths and weaknesses but it’s important to ensure that no character’s strengths or weaknesses are too much, because that causes a ton of complications in gameplay.
Easy judgment: it’s definitely imbalanced at 1st, 2nd, 3rd, 4th, and 6th
At these levels, you gain absolutely no benefit from the trait, while still taking its rather-massive downsides. If you were only playing at these levels, you should obviously never take this trait.
The fact that this level-dependent behavior exists at all is a big problem with the trait, in my opinion. Every other trait gives a small, static penalty and bonus. They don’t scale with level—which means that as the character levels up, the significance of their traits is watered down. That makes them much easier to judge, since we can look at them at 1st and if they’re OK at 1st they’ll be OK after that because they’re only going to get relatively smaller from then on. With this trait, instead we have to consider all kinds of level ranges.
At 17th, 19th, and 20th: Up 3 feats, for somewhat less than 3 feats’ worth of downside
Improved Toughness from Complete Warrior (and elsewhere) gives +1 hp/level. It’s a pretty poor feat, not often recommended for any purpose. Certainly better than Toughness but that’s not saying much.
Great Fortitude, Iron Will, and Lightning Reflexes each give +2 to a single saving throw, and are very poor feats only ever taken when required for something else. Getting +1 to all saving throws, for a total of +3 worth, is not really much better, if it is at all.
+1 to all ability scores isn’t available, even approximately, via feat—feats shouldn’t and mostly don’t touch ability scores. That said, if it was available as a feat... I don’t think a lot of characters would be best off taking it.
So the downsides are, roughly, worth the negative of three poor feats. All together, they might be worth two feats, but definitely not really worth three. So when, at high levels, you have three feats more than someone without this trait, you have a winning bargain. At those levels, most characters should probably have this trait, optimally speaking.
We can maybe extend this to include 11th and 13th through 16th, too, when a character with this trait is two feats ahead. I can imagine two feats being worth these downsides.
Beyond that is harder; one feat for these downsides? That’s a whole lot harsher, and dubious.
The elephant in the room: SAD vs. MAD
So the biggest downside, by far, is the −1 to all ability scores. That’s painful for anybody.... but it’s not equally painful for everybody. Which brings us to the really, really big problem with this concept: single ability dependency versus multiple ability dependency.
Single ability dependency, or SAD, refers to relying on just one ability score to make your character work. Think Intelligence for wizards or Charisma for sorcerers. Other ability scores may be nice—no one wants to have a poor Constitution—but really, just the one is crucial.
Multiple ability dependency, or MAD, is when you need more than one ability score. Think Strength for fighters, except they also need Intelligence for Combat Expertise and Charisma for Intimidate, and if anything need Constitution even more than the wizard or sorcerer. Or for that matter, look at monks and paladins, who absurdly need tons of ability scores—no paladin can really afford to skip Strength, Constitution, Wisdom, or Charisma, and monks are really hurting unless they have quite-good Strength, Dexterity, Constitution, and Wisdom.
That means that a wizard or sorcerer loses, basically, −1, maybe −2, in total to scores they actually care about, while a fighter might lose −3 and a paladin or monk might take −4. It’s no coincidence that the classes that are SAD are magical, while the classes that are MAD are mundane. It’s also no coincidence that the SAD classes are the most powerful in the game—nor that the magical classes are the most powerful in the game. Being MAD, being mundane, being relatively weaker than other classes, these things all come together.
Another non-coincidence—the classes with the most bonus feats, and therefore the least upside from this trait, are again those same classes hurt most by it.
So what you have here is a trait that is painful to take, but less painful for the classes who see the most benefit—who are also the classes that were already the strongest. I think it’s really pretty obvious why that is a problem.
Ultimately, I don’t think this is the right approach, or something that can be made into a good idea.
You can offer another bonus feat, right from 1st perhaps, which would go a long way towards making the trait palatable at low levels. Especially since 1st-level feats are sometimes special things that are nice to have extras of. Would make things even more of a problem at high levels, but you say you don’t often reach them, so maybe that’s not worth worrying about.
But then everyone should take the feat, unless they’re a MAD class that already gets a lot of bonus feats and they’re looking at this hurting them more than it should while giving them less relative benefit than it does everyone else. That’s not good.
And on top of that, it’s just so big, it’s not a trait at all. Putting it in the trait slot is just strange. Unearthed Arcana has a system for getting extra feats for some downsides—those are the flaws. At least then everyone can take the extra feats, choosing flaws that fit their character well—flaws aren’t balanced, not by a long shot, and will make characters more powerful, but the internal balance is a whole lot better.
So really, I just recommend using flaws for this.
