Custom software has already fixed #1 and #2 and #4. They tried to improve #3, but there is only so much you can do.
1) By custom you mean custom kernel. Custom kernel is only going to help you where the CPU is the big drainer. So yeah, you can have it ramp less aggressively, although conservative governor will already achieve most of that. Where the Nexus 4 suffers big time is in its use of the radio. Brian mentioned in his One review that the use of network batch operations helps give the One great battery optimization. He also mentioned (via twitter to me) that other OEMs have mentioned that AOSP lacks this optimization. While it is in the Android developers guide, it's really app dependent, and so HTC and other OEMs apparently go and enforce this on a system-wide level. There's probably other optimizations they do. Custom ROMs and kernels don't really touch this.
Either way, remember things like wifi and 3g browser test don't use that much CPU power. You're not actively kicking mpdecision on so that it's ramping 2 cores to 1ghz. Yet the Nexus 4 flat out sucks in those tests compared to the competition.
I mentioned in my Battery Life thread that it'd be good if we could benchmark the Nexus 4 running Franco kernel with those battery life tests that Brian runs. That's the only way we know how much battery life has improved.
2) Yes custom kernels solve this, but it'd be good if everyone got a decent calibration out of the box. IT doesn't have to be iPhone 5 good, but maybe something like what the OEMs do. Even the Optimus G's calibration is 100x better than the Nexus 4's.
3) It's clear the Nexus camera is lacking in quality. But besides the quality improvement, we need other features like burst shooting. Right now the Nexus 4 does like 1fps? The past HTC cameras shoot faster than my Canon Rebel T1i. Maybe like 4fps is reasonable. Or even 3fps would be nice. On top of that maybe IS or whatever nifty features other manufacturers are implementing. I'd just like the next one to at least beat the GS3... yes GS3, not GS4. It's sad that the N4 can't even outshoot the S2 already.
4) Red LED of death isn't fixable by custom software.... I myself experienced it and there's a good number of threads out there. Plenty of RMAs. Buzzing earpiece is fixed by software? I didn't have this one on my first Nexus 4, so I never really paid attention. I only noticed it with my RMA one.
Anyhow, I think 1 and 3 should take a little work, and I'd like to see a more polished product, rather than what they can rush out by May, which I suspect would not be sufficient if we stack the new phone up against the new competition.