In good news, this is totally normal. My daughter especially never used toys the way they were "supposed" to be used. Puzzle pieces were cookies, stuffed animals were babies, etc. In fact, she never really played with toys much at all. Still doesn't. My son is a little bit more hands on with his toys, but they basically only do imaginary play. He has a whole bunch of racecars, and he'll line them up and play with them on the track for about 5 minutes. But play "baby" with his sister? That can last forever (they're 5 and 3, by the way). Right after Christmas their favorite game was to play "Christmas," which was to take every single toy in the playroom, pile it all up in the corner, cover it with a blanket, and then pretend Santa had come. While I'm normally pretty easygoing, that game had to stop right away! I mean, how many times can you put stuff away?!
My best advice is to encourage him to play the way he wants. After all, it's _play_. It's supposed to be _fun_. He has years and years and years ahead of him where he's going to have to do things "right."
But I do understand how frustrating the clean up can be. My advice there is to work on making it a game. He won't always want to play, of course, but at this age, he's still going to need a good amount of help cleaning up anything. Think of all the different ways you can sort those piles - by category, by color, by size. I normally make it a race (i.e. I bet I can pick up all the blue cars before you pick up all the red cars!). That helps a lot.
See also if you can help control the amount of stuff that gets pulled out by playing along. So if you pull out the play tent, tell them they have to get to the imaginary island by boat, and they can only take the stuff that can fit in the boat - then give them a laundry basket boat and tell them that they can only fill it once or it will sink. Don't know if that will work, but I find my kids are much more compliant if they feel I'm playing along.
Finally, remind him as he's pulling stuff out that he's going to have to clean it up, and then be consistent in making him help clean it up. Sometimes now I can get them to not "dump" quite as much stuff by saying "remember how you had to clean all that up yesterday? Let's not make quite as big a mess today."
Most importantly, relax about this. In no time all he's going to want to play with is a handheld gameboy and you'll miss the piles of legos and shoes and adventures with dragons. Good luck.