Well there are various radio devices that just take 2 pins, and I don't think they need to be PWM or analog pins. Be sure to check whether what ever devices you use are legal for your area. The following are some devices legal in the USA:
- OpenSource RF - http://www.opensourcerf.com/
- RadioBlock - http://www.kickstarter.com/projects/545073874/radioblock-simple-radio-for-arduino-or-any-embedde?ref=category - note this is a kickstarter project that if it gets $18,000 by October 6th, it will send as rewards the number of units you backed. I am a backer for 2 units. Note, experience has shown that the dates of delivery from kickstarter projects can be wildly inaccurate, so if you need something immediately, go with a more mature product.
- Bluetooth - Sparkfun and others sell bluetooth modules directly for lilypad - Bluetooth Mate Gold - WRL-09358 - SparkFun Electronics
The other thought if you want to still do IR, is have a second board that only does IR and has a serial/i2c/spi connection to the board running the show. Obviously if you get into multiple boards, you could share some of the PWM support across the boards.