It hasn't changed that much. You can infact use exactly what Edward suggested. Many of us have upgraded to either the R420 or r700 reader. Most use panel antennas either side mounted or on a truss.
I have used a matt. It is a poor choice for bikes for many reasons from safety to durability to read accuracy (almost impossible to get a decent attack angel on the chip from a matt.
As for tags, lots in use. I agree with Jon Rosen, the M750 dogbone is about as good as it gets for passive RFID. Our read rates are significantly better than with R6 based chips. My guess is that Higgs9 chips would also be good but I don't have any experience there