Intel has a much more efficient architecture that allows their cores to do more work for each clock cycle compared to AMD. As a result, Intel's cores are about 40 to 50% faster than AMD's and will be about that much faster when looking at an AMD CPU at similar clockspeed and core count.
Another factor is AMD's current architecture has shared resources that can slow things down for them, AMD pairs two cores into a module which has two integer cores and one floating point unit. Intel has 1 integer core to each floating point unit and no resource sharing. As such, an FX 8350 will only have 4 floating point units, and is effectively a quad core CPU as far as floating point math goes, while somthing like the FX 4300 is a dual core when doing floating point math and an FX 6300 would be a three core CPU in floating point operations.
AMD's big problem, aside from not releasing any new high performance CPUs in more than three years is most software simply isn't written to work all that well with their architectural decisions. AMD tried to compensate for their poor per core performance by putting more integer cores onto the CPU, and that works well in certain tasks like video rendering, but it doesn't work so well in applications that primarily use one, two or three cores effectively like most games. Between an architecture that simply isn't designed to meet the needs of most consumer software and AMD not releasing anything truly new outside of low end, low powered products, AMD has fallen pretty far behind in terms of performance. Overclocking AMD's CPUs can help them stay somewhat competitive with a stock clocked Intel i5, but at the cost of generating a lot more heat and using a lot more power. It's why you won't see a lot of people recommend AMD processors anymore outside of extreme low budget gaming builds, and low budget rendering builds.