I would say u made the wrong decision to me.
and ofcourse the shop has to mark up to earn some profits.
the reason i guess he asked for trade is because 6D is easier to sell than the older 5D2 and moreover yours come with warranty.
The 5D2 should be similar to the 6D in terms of functions although the 6D is very much the entry level budget FF option for consumers. The 5D2 was probably something that was used by quite a few professionals back in its day so the shop is not entirely wrong when they say the 5D2 is more of a pros' camera than the 6D.
The thing that stinks about this is the feeling that the second hand shop you sold your 6D to did not seem to be entirely upfront, choosing to be selective about facts and putting things into context.
My suggestion is to forget about trading again with that shop unless you really get a good deal on the 6D which you have just sold. Plus please bring along another friend or two who really know their stuff well. Otherwise I would cut my losses and get a 6D off BnS, assuming you know how to check for flaws.
it is really hard to say which camera is better,but if u asked me probably both are similar or on par to me.
some things are good in 5D2 and some are good in 6D so it is the person who looks at which factors are more important in a camera. and also 5D2 is pretty old model and have u checked on your shutter counts? If shutter counts is more than 50K,i would dare to say u have downgraded.
He said was over 8k. Now im wondering it if is rigged. Scary.