RFID system to detect a specific object 50 cm away
50cm is more than doable with UHF EPCglobal Class 1 Gen 2 (ISO 18000-6C) RFID Tag.  These operate in the 870-930 MHz ranges, depending on area of operation.  These are actually made to be read at a distance.  

A folded dipole tag with decent read range (assuming it is not next to metal) would be about 1.5-2" long and 0.5-0.75" wide.  We are using an RFID chipwith an PCB antenna that is around this length and getting +1m read lengths.

Read range is over a 1m with a fairly low powered reader.  You have to get polarization of the antennas aligned, or use a circularly polarized reader antenna.  We have seen some pre-made serial reader modules that are 1"x1" or close to that.  A reader antenna inside 2"x4" is tight, but for only 50cm most likely doable.

There are also some EPC Gen2 readers available now that function like the Square credit card reader, using the mic input as the data line.  Here is one of these guys: http://thinkify.highwire.com/product/arete-pop-rfid-dongle-reader

For an embedded micro type application, I would go with the easy to interface with serial controlled modules.