This is an interesting choice with the current sale--one I've thought about, too. I wish KEF disclosed the full spin data, as we only have DI for Amir's measurements of the R3.
The R5 doesn't seem to follow the typical bookshelf vs. tower tradeoffs. It isn't more efficient than the R3, and it doesn't seem to have more bass extension (to get some of those gains, you need to go to the R7). You're likely going to want dedicated subs with either the R3 or the R5. Also, unlike a lot of bookshelf speakers, the R3 is a three-way, so gaining a dedicated mid-range is not a reason to "step up" to the R5 (compare the Revel M106 vs. F206).
My guess is the R5 was intended to be the tower version of the R3. Some folks just don't prefer bookshelf speakers. I love the look of the R5 and would much rather have it in my living room than the R3 on stands.
Something else to consider. The tweeter on the R5 is not at the top of the speaker. In my room, it would placed well below seated ear level, and would need some base platform to lift it. With the R3, you need stands anyway for the best sound and probably can find the specific height for your room. To me, that made it easy to pass on the current R5 sale.
Finally, hear's another way to look at it. Based on available data, the R3 is one of the best performing speakers in the world (with a sub). KEF's data indicates the R5 is in the same class. There are some tradeoffs with KEF's unique Uni-Q array versus other designs, but between the R3 and R5, you probably can't go wrong!