How about building encounters based on the plot, the nature of the adversaries you have been using, the guestimated strength of the party, the terrain/environment and some good judgment? Who the hell actually played with 1 fighter, 1 rogue, 1 cleric and 1 wizard? I have yet to meet that game group and bet I never will. CR was predicated IMO preposterously according to this setup which is extremely limiting.
I played AD&D, and 2e and there was no CR or anything except some sort of monster level scheme that maxed out at Level 10 monster...needless to say, not much of a help. The fact is that encounters should be keyed to a variety of factors above and beyond CR. The DM will make some undermached and overmached encounters and THAT IS GOOD. Players should not have any particular expectation of automatic victory, they shouldn't be able to calculate, "Hey this encounter drained exactly 25% of our resources, cool."
DMs will have to use some trial and error. Amazingly I, and others, have been able to run successful campigns lasting over a decade without needing CR.
Sundragon