There are many perks in Fallout 3 which simply increase one or two skills. On paper, these perks simply look like places where the developers ran out of good idea. But in use, these perks are very important to your character's development. Not all perks are worth taking, and even less perks are worth taking for a certain kind of character. Someone who uses Small Guns won't be interested in perks that increase Energy Weapons, and a stealth character probably won't be interested in perks that increase health and survivability, instead choosing ones that increase damage.
As a result, you'll probably find many levels where none of the perks look tempting. If that is the case, then skill-increasing perks are a great choice, because by taking them you increase the overall pool of skill points that your character has. There is no benefit to increasing a skill past 100, so skill points gained by perks gives you additional skill points to put elsewhere. Now obviously you don't want to take a skill perk if you have absolutely no use for the skill in question. The perk that increases Barter and Speech skills is a good example of this - Barter is always worthless, so that skill perk is terrible. However, as long as the skill perk provides points in a skill you plan to use either immediately or in the future, it is a great investment. Take Size Matters, for example. Using that perk, you gain 15 skill points in Big Guns. As long as you intend to use Big Guns, that is a wonderful perk. It means that you have gained an additional level of skill points overall, provided your character is of average intelligence and would typically gain 15 skill points from gaining a level. Those 15 skill points can be put somewhere else, like Science or Speech, resulting in a character with more well-rounded skills.