If you don't have clients that have 3 antennae (or, the ones that do are not used constantly for high speed transfers within your network), then the RT-AC56U is better because;
The RT-AC66U is based on the equivalent hardware as the RT-N66U. Slower processor and a much older 'AC' design (first gen).
The RT-AC56U is based on the equivalent hardware as the RT-AC68U. Faster processer, better designed radio circuitry (as witnessed in range and throughput in actual, real world, use).
And that is even with it's internal antennae.
If you think the internal configuration is hindering performance or range,
http://www.snbforums.com/threads/asuswrt-merlin-3-0-0-4-374-38-is-out.14691/page-19#post-99500
http://www.snbforums.com/threads/asuswrt-merlin-378-55-3_hgg-final-mod.26524/page-2#post-199549
As to whether you should replace your 'AC66U with an RT-AC56U? Not without testing fully in your environment.
But you will get a few more features to use that the older router can't handle because of the lower performance processor it has (AiProtection being one such feature, for example). You should also get faster VPN speeds as well.
If you can use your 'AC66U as an AP to light up a remote corner of the areas you use WiFi in, this low cost 'upgrade' is a no brainer, imo.
If you want a single router that offers more of everything that your 'AC66U can do and more, the RT-AC3100, RT-AC88U and the RT-AC5300 are the better long term options if you're really pushing your network and you have many 3 antennae/3 stream clients that you use to the max.
Of course, you could also wait for the latest Asus batch of routers that will be introduced soonish too.
This is a game that never ceases to be fun (and expensive).