I once met a man who was a member of a whisky club, this was in the days I was myself fairly new to whisky, who assured me independent bottlings were always superior to the standard distillery bottlings. I strongly disagreed with the man. I guess I still do, although I can see his point.
A standard bottling is created in a totally different way from an independent bottling. The distillery is looking for consistency, so they use their entire stock of casks to compose the same (or very much the same) whisky every time. Their brand is associated with a specific taste, and they have to reproduce this every time. Sometimes they make a limited or exclusive series, which is unique but in the general direction of their standard product.
An independent bottling is unique every time. The independent bottler has a much more limited stock of casks from any given distillery and usually bottles one cask at a time. This bottling's quality depends on that one or two casks it was made from, so there is no way of balancing a lower quality cask with a better one. Of course (most) independent bottlers select the casks, they want to bottle for quality, (yes some will just bottle anything).
So it seems reasonable to conclude that a standard distillery bottling has a consistent quality, and an independent bottling can be better or worse, depending on the casks they bottled.
As a connoisseur a standard bottling is good, but since it is the same every time, it seems more interesting to explore the wild variety of a plethora of independent bottlings. Sometimes they may disappoint, but there is also the very real possibility of finding a hidden gem.
The man from the whisky club claimed independent bottlers would only buy the high quality casks from distilleries and therefore each of their bottles would be better than the distiller's. It seems highly unlikely to me a distillery would sell only their best casks to an independent bottler. Furthermore, this claim relies on the fact that bottler's would buy matured casks from the distillers. Most of the time it works the other way around. Bottlers, typically blenders, have filling contracts with distilleries, or buy unmatured casks, and only years of maturing will prove it to be bad, average, good or perhaps even great. Douglas Laing co., as a blender, has filling contracts with distilleries, and opts to bottle some exceptionally good casks as single malts, and the rest goes to the blending. Gordon & MacPhail even mature most of the casks they buy in their own warehouses.
A bottler isn't always assured of getting only the best of casks, and so he faces a challenge : what to do with casks that are sub par? As I already mentioned, some bottler may deal with this challenge by ignoring it and bottling it anyway. Others, such as Douglas Laing, just use these for their blend, and others still, such as Gordon & MacPhail, have large enough stocks and the know-how to combine several casks to get a good quality result.
If you want to buy an independent bottling, you as a consumer face a wager, will this bottling be worth the price you pay for it? There aren't many guidelines. Not much on a whisky's label can tell you about what you will find inside. Distillery? If it's only one or two casks they are no way guaranteed to taste anything like the distillery's standard. Age? Given that every cask reaches a peak in quality, and that this peak is different for every cask, age is no useful guideline at all. Vintage? Is of absolutely no consequence. The type of cask may give you some general idea, but doesn't assure quality at all. In the end you'll have to rely on the bottler. Is he committed to bringing high quality products to the market, or is he just interested in another sale. Knowing how the bottler operates helps, but nothing beats experience. If a bottler hasn't let you down, time after time, it's not likely you're going to get rubbish the next time. It all comes down to reputation.
I want to note that some distilleries' standard bottlings are so varied that it becomes hard for the customer to discern a typical taste or nose for that distillery, I'm thinking of Bruichladdich, Glenmorangie, etc. Whether this is commercially a wise move, only time will tell.