My current working Hypothisis - Is this really a Battery Charging issue?
The more I participate in this thread, the more I am leaning toward this being a Battery Charging issue rather than a Battery Usage issue.
I say this for lots of reasons. First, I noticed that it takes longer to charge my battery in Lion that it took when I was on ML. This is important because Lithium Polymer batteries are very particular about how they are charged. And, an improperly charged battery could result in the two problems reported in this thread - diminished battery capacity as observed by the battery draining quickly and a drop in battery health from 100% to a number far less than 100% within just a few charging cycles.
In addition to my personal observation about the charging time on the various OSes, another big clue appears to come from A-3's posting which doesn't make sense in terms of the percentage drop per minute or the remaining time as computed by the OS. It's not clear how the remaining time is computed - whether it is derived solely from amperage (mA) remaining, or if their algorithm also considers the voltage level of the battery. Since both values are used (or should be used) in charging, it is possible that both are used in determining reaining time.
One final reason I lean in this direction - that it is a battery charging issue - is because Apple's FAQ on batteries gives advice that runs counter to the advice given by manufacturers of LiPo batteries. I don't want to get into a p*ssing match about whether Apple is right or wrong. Anyone who can look at Google can find what the manufacturers say and what Apple says. So, if Apple is right and they have "special" batteries, that's one thing. But if they are treating LiPo batteries in a similar to NiCd or NiMH batteries (in terms of how they are charging them), then that would be a problem.
In either case, this hypothisis is relatively easy to test; but it will take someone who is on ML and having the issue to do it. It will also take someone on Lion (or ML) not having the issue.
First, report your battery capacity (mAh), current usage (mA), % remaining, and reported time remaining in 10 minute increments. This will enable us to determine if the change in mAh over a period of time is consistent with the reported draw (mA) on the battery over that period. Note: When on battery power, mA will be a negative number.
Second, drain your battery to something less than 80%. Then put it on the charger, every 10 minutes check and see what the reported current usage is (mA) and the charged capacity (mAh). The mA value will be a positive number. Do this until the battery is 100% charged and the mA changed to 0. Also capture the total amount of time it took to charge the battery. Note: When your battery is charging, mA will be a positive number.
Depending on what we find in these two experiments, we'll know if what is really going on is a Charging Issue or not.
P.S. Hey Apple, if this really does turn out to be the problem and this helps you sole it; how about you throw a few 13" Retina MBP's my way!? :-)