Dear Julie,
This is a difficult problem, but maybe some general advice would be helpful.
First of all, just to get this point out of the way -- many relationships are a mystery to the outside world. People have all sorts of private needs, loves, fears, compulsions etc and it's of course impossible to form a complete picture of the "suitability" of a match from the outside. Maybe he's a slob and a loser to everyone else, but gives her such unconditional love and support that she's able to be much more ambitious than she would have been with a more hardworking and less attentive mate. --- You get the picture. But while it's important to point this out, there are also many relationships which are genuinely destructive for the people involved; let's assume your friend is in this situation.
I think it is difficult to overestimate the effect of a (long-term) bad relationship on one's quality of life, dreams, hopes, ambitions. Our lives are largely built up from the fragments of daily life, a kind of continual sedimentation, and our greatness -- or potential for greatness -- is intimately bound up with the energy with which we face the world each morning, with the day's constant presentation of possibilities, and how we choose to respond. (Conversely, of course, there is something very powerful in life which arises from satisfying relationships -- romantic or otherwise). Subtle but relentless.
I assume from your post that your friend's life is not in danger. If the relationship is overtly abusive, everything changes. Call a local abuse hotline for advice right away. Otherwise, I'll continue:
The women I have known in bad relationships fall broadly into two categories, which sometimes overlap. First, there are those who remain in the relationship out of some kind of inertia -- perhaps they are somewhat cynical and don't think others would be so much better, perhaps they fear the social stigma of being alone more than they dislike their current partner, or perhaps the relationship just works like a slow poison --- no single moment seems to them terrible enough to warrant the break, even if the cumulative effect is awful.
Second, there are those who really are somehow wounded. They find themselves attaching to partners (and often it is not just their partner) who reinforce certain negative feelings they have about themselves or the world. Often, they are replaying dramas from adolescence or childhood, or their own parents' lives. This may sound a bit cold to say, as obviously everyone has wounds, and life is quite an intensive learning process! But some wounds (or rather some manifestations) are much more immediately threatening to the person's life, or quality of life, than others. And the reality is that changing this requires, at some level, a real commitment on the part of the person involved to challenge certain deep fears and behavior patterns, which is obviously difficult work. Even before this, it requires awareness.
I do think you should try to say something to your friend, even if at first it is fairly tame. For the moment, focus on her. If you don't feel you can speak frankly about her partner, try gently criticizing certain behavior patterns, or encouraging her to laugh about it (you can tell some mean jokes about your boorish uncle Joe). Without being self-righteous or assuming you know what's best for your friend, you should nonetheless recognize that sometimes friends see a person's potential and gifts much more clearly than the person themselves. When this happens, it is a basic human courtesy to let the person know that you appreciate their talents and hope going forward that they will develop them further. You can never assume that someone is aware of their gifts or qualities -- even very superficial and obvious ones. Many women do not, in any deep way, feel beautiful. When it comes to abilities and talents, the situation is even more complicated.
In general, my advice for your friend would be that you try to encourage her to get involved in as many situations as possible which reinforce the positive character traits which you feel this relationship is suppressing, e.g. self-esteem, ambition, positive body-image, etc. Sometimes, an effective first step is simply to show the possibility of living otherwise. You might find her a good mentor in her career, organize a dinner with some older married friends whose relationship you really admire, or encourage her to make new female friends or to join a gym. You can use the excuse of a bachelorette party for a frank discussion of the ideal relationship. New friends who might blurt out their disapproval of this boyfriend are also useful! Ideally she would be surrounded by a group of supportive friends and colleagues, not just you, as she makes these very important decisions about how to live her life. The process of rebuilding one's self from the ground up (you don't want her to dump him just to find a clone) is a long, though rewarding, one.
Good luck!