I don't know that you can really get into a comparison of factory vs aftermarket as tray points out the lines are pretty blurry....
rev10's are considered aftermarket on some boats but are factory on others. jl's are factory now on supras but you can still pick them up in the aftermarket.
amp tuning is really the only thing that you could say is factory about any of the systems anymore as in some cases they are boat-specific however even those have non-factory equivalents that you can buy, just not tuned as such.

boats are really nothing more than a factory hull cobbled together with a lot of aftermarket parts.

I do agree with matt in his review of the ws hlcd drivers. rev10's/410's sound like $hit to me- way too much highs. do they work at wakeboard distance better than most? ya but at a cost of sq when you're surfing or just chillin in the boat. all imo and based on the number of rev10's running around, others think differently.

harkens me back to my old circuit city days as a sales manager.
you want it loud? dcm or klipsch for their 12-15" subs and hlcd highs. pick any receiver that has a ton of power, usually sony or pioneer as they were clean enough.
you want it clear? infinity or polk. smaller subs and actual tweeters. usually sold onkyo or HK receivers as they were considered more musical but less power for same $$.