I liked 28 Days Later enough that I really didn't expect to like 28 Weeks Later but it overcame my expectations. I still like the first better and the reason has to do with exactly the question you ask. 28 Days Later stood alone as a good story, 28 Weeks Later seemed specifically designed to lead into another sequel. If they weren't intending to bother with another sequel the plot of the second movie probably have been completely different. Don't get me wrong I like both movies and I will see the third.
I like them both but 28 weeks later was to short and I think thay sould make a third one that would be like 28 Months later. But 28 days later was good too.