I am surprised if the TB has battery issues that bad.
I mean come on, battery life is known in the design phase and is verified and tested very early on in development by HTC.
Also the Snapdragon in the TB uses the 45nm manufacturing process (called "2nd gen") as opposed to the earlier (also identical 1GHz clock speed) chip in the Evo 4G CPU. The EVO 4G CPU also a Snapdragon is made using a 65nm process and is labeled "1st gen".
Comparing equivalent Snapdragons in that entire line up of chips between the 45/65 process, Qualcomm stated that change provides a 30% lower dynamic power consumption and a much lower standby power as well. The battery capacity reduction from Evo 4G to Thunderbolt is only about 7%. This should guarantee an overall longer times between charges with the TB (of course under identical use). Adding an aftermarket higher capacity battery of course would also help. Now that being said the Evo 4G battery life is pretty bad.
BB also published a talk time for the TB at 6.3h, see below. Now that being said the reliability of anything on the TB from BB is questionable...
Yes but the EVO has 1500 mah battery and the TB has a 1400 which could definitely cause some problems.