The Superhero Database Classification number, or SHDB Class, is a number that represents the overall 'power' of a character. All traits of a character are used for calculating the Classification.
What it DOESN'T mean
This doesn't mean that a higher class would always beat a lower class character. But the bigger the difference in Class is, the more obvious it is who'll win in a fight.
How is this calculated
( INT^1.3 + (STR*0.5 )^2 + (SPE*0.5)^2 + DUR^1.6 + (POW + (SPS*SPL))^2 + COM^1.8 ) ^ TIER
Super Power Score and Level
Every Super Power has a score (SPS) that is used to calculate the Class. Each Super Power also has 3 levels (SPL). The level is set when connecting that Super Power to a character. The level determines the final score, of the Super Power, being used in the calculation.
Sure, Snake possesses an IQ of 180, knows six languages, and has done things like defeat Big Boss with nothing but a lighter and hairspray. Unfortunately, that pales in comparison to Batman being the second most intelligent human next to Lex Luthor, and we all know how dangerously intelligent Luthor is. Now, Snake is arguably stronger, faster, and tougher than Batman. However, it's really nothing new that Bruce has dealt with. Even if you were to give them preparation, Batman would make the most of it since he's been able to place Wonder Woman in an endless fight. Solid Snake is definitely a master of CQC, but he doesn't possess the same experience that Batman has in that field. Bruce has mastered over 127 martial arts, and that's more of the training than David's ever had.
In the end, David's outclassed.