Because we need a loli bait character and it's easiest to put it as the MC's imouto. Considering they're often weak satelite characters, you'd have even weaker satellite characters of satellite characters if we're going this way.
Though in all seriousness, you will notice the character relations getting a lot weaker except in the most well written of anime. Hell, there's so many anime where anything but the canon couple is just a set of loose strings.
Bascailly, if you're not a main character in many cases, you don't get to have a cute little sister, a girlfriend that matters to the plot, or even closure.
Though any number of series will buck the trend. But in general, it's an utter lack of care.