would it be cheaper or worth while to only do two channels?
Cheaper: probably...just ask Frank/Busman or the Oade Bros.
Worthwhile: Probably no, IMO, at least if you get a regular R-4 vs. a R-4 Pro.
With the regular R-4, if you do not mod. one pair of inputs they will really only be suitable IMO for either SBD feeds or when using an external pre. With the R-4 Pro, that could be worthwhile if you do not mod. chan. 1/2 providing you plan to always send the R-4 Pro a digital signal via AES/EBU. You could do that and send SBD feeds to chan. 1/2 until you have a chance to pick up a pre/A>D with an AES/EBU out (V3, MiniMe, Benchmark AD2k+, etc.)
With both the R-4 and R-4 Pro, the digital input overrides the analog inputs for chan. 1/2, though the digital in is worthless on the regular R-4 since it resamples the signal (just like the UA-5).
On mine, I have the Warm mod. on chan. 1/2 and the transparent on chan. 3/4. That way, I can still use the T-mod chan. 3/4 for SBD feeds and have the choice open to either run a pair of my AKGs through the W-mod chan. 1/2 or to use my MiniMe and send a digi signal (+ clock).