Biggest difference is amplification. The VSX-53 uses Class A/B amps while the newer SC-1222 uses Pioneers Class D3. The Class D3 amps are also 4 Ohm rated so most likely they are a little more robust and able to drive speakers of lower impedence. While the VSX-53 is no lightweight, its best to stick with speakers of a higher impedence - 6-8 ohms. The 53 gives you full band phase control; the 1222 does not. The 53 gives you two HDMI outputs; the 1222 only one. Finally, the Elite 53 gives you a 12 volt trigger to power up external components like a power amp. The Pioneer SC-1222 has no such trigger.
Beyond this, the rest is cosmetic. Do you like a blue display with red lights (the 1222) or an amber display with blue lights (the Elite 53). Do you want a plastic faceplate (the 1222) or an aluminum one (the 53). Finally the 1222 comes with a 1 year warranty, the 53 has an Elite 2 year warranty.
While both have a full set of pre-outs, if I already had or planned on using an external amp,I would choose the Elite 53. If I had no intention of using an external amp, then the 1222 in a heartbeat to get the superior internal amplification.