clock for clock
Atom uses in-order-execution, like an ARM A8, which currently only goes as far as about 1GHz, at least in current devices. Clock for clock Atom and A8 are going to be pretty similar, since the Atom here is quoted as going up to 1.5GHz. The x86 overhead is probably pretty small nowadays compared to the rest of the processor.
The Coretex A9 will use out-of-order execution like an Intel Core-type chip and hence be potentially much faster than A8. Out of order execution is great, but it comes at the cost of transistors for lots of pipeline logic.
I'm not knocking ARM or their implementors, they've done a lot of good work, but there isn't a 'secret sauce' that magically makes ARM better than Intel any more than anything that magically makes a Core i7 magically better than an AMD part. Intel was behind AMD in both desktops and servers for a while, but they caught up. Intel could catch up in smartphones too.
Intel also has the advantage of being very good at fabrication, getting power efficiencies out of die-shrinks that competitors find difficult. Again, though, that's not a secret sauce: Intel just has scale on its side.