The only 2 settings with a mentionable number of test results so far are --(alt-)preset standard and ~128kbps ABR/VBR. Details:
--(alt-)preset standard:
In the tests with 3.96beta1
here 3.90.3 won on 13/17 samples. This would be a "p-value" of 2.5%. ~ 50% of the samples tested were known lame 3.90.3 problem samples so one could assume a slight bias against 3.90.3. OTH the samples didn't really cover a broad/representative variety of music. Anyway, 3.96 would need to be better on at least 50% of samples tested - and it's a long way till there, no matter what type of music samples tested in future might be.
The only change between 3.96 beta1 and final for --preset standard was the minimum bitrate set to 128kbps. The 4 samples that were tested after this change were still worse then 3.90.3.
Conclusion: Surely it's too early to tell, but it's likely that 3.96 isn't better then 3.90.3 with --(alt-)preset standard setting, probably it's worse - so for this setting 3.90.3 has good chances to stay the recommended version.
~128kbps ABR/VBR:
Here it's the other way round. It looks like 3.96 with --preset 128 but also with -V 5 are better then 3.90.3 --alt-preset 128. If --preset 128 or -V 5 will win (and if there'll be a clear winner at all) is impossible to estimate right now.