Honestly, I would run it. Let one station run everything and simplify the network.
Unless you need the second one for wireless extension, then I wouldn't even bother.
I need the second AEBS as an extension to reach the bedroom over the garage (far end of house) where my son has his Macbook Pro and Gaming PC. The MacBook Pro can reach the far router albeit with very low signal. The wireless adapter on the PC (TP Link Dual Band adapter) can not reliably see the far router on the 5GHz band.
----------
Make sure all the connected machines have time machine back-up turned off (if you're using a NAS.) I've found that messes up my extended network when working with video files off a server.
YMMV
I do have a 2TB disk connected to the main router that serves as time machine for all the Macs in my house. But that is not the issue. If I run the transfer test with the 2 routers in series I get the 11.5MB/s. If I immediately take the second router out of the picture (using the same CAT5e cable direct to the Mini) I immediately get 108MB/s. If time machine transfers were getting in the way I would not expect such a consistent jump.
My guess is that the 11.5MB/s is the effective transfer rate for 100baseT (Fast Ethernet). 108MB/s is the transfer rate for 1000baseT (Gigabit Ethernet). When connecting my 2 routers in series I am getting knocked down to 100baseT somewhere in the path. Both the mini and the iMac are reporting that they are connected at 1000baseT in the hardware information. So I guess it must be in the link between the 2 routers.