I think true cloning of a beer is entirely possible. The ingredients available to homebrewers are exactly the same as what the commercial brewers use. A lot of commercial brewers freely give out their recipes. So I figure it's worth a shot trying to duplicate my favorites. I have brewed numerous clone recipes in the past, and while I never actually cloned one IMO, I always figured it was my own fault for not trying hard enough, as I rarely brew the same beer twice, always wanting to try something new. However that's about to change, as I've set my heart on trying to clone two beers, Anchor Porter and Pete's Wicked Ale, which I'll be working on in the next few months. Now of course they don't make Pete's anymore, so the "cloning" bit will have to be based on my taste memory. But the Anchor, I will compare side-by-side with the real thing, brewing it at least twice if not 3 or 4 times, tweaking each time until it tastes exactly the same, if possible. Even if I can't clone it, I think it will be fun to try and a great learning experience.
I do think an important part of the cloning process might be in aging your beer for several months. When you brew your own, it is super fresh. When you buy it at the store, it is probably already 4 months old or more (at least by the time it gets to the front of the shelves in Wisconsin). So it's only fair to compare "old" homebrew to "brand new" store bought beer, otherwise you're not comparing apples to apples. Then of course after you think you've cloned the beer, you'll need to decide whether you prefer to drink your clone young or aged, and this is largely subject to personal preference. I guess what I'm also saying is, it's entirely possible to clone a beer and not have it taste exactly the same as what you buy on the shelf. Your own homebrew might be a clone but taste even better than what you can buy, due either to freshness, or to slight tweaks that you have done with the recipe, or both.
All in theory. I haven't cloned a beer... yet... but I do think it is an excellent learning experience, and the potential benefits are great, so I am going to try.