Low quality micro tools and miniature end mills have problems that may make the higher-cost end mills worth the expense. Much of the cost difference has to do with two factors: the grade of carbide being used and run-out caused by poor manufacturing. This is what you should know.
More Carbide Equals Longer Cutting Power
End mills are made of a combination of tungsten carbide grains and cobalt, as a cementing material. The tungsten carbide is the substance that retains the sharp edge you need on the end mills, while the softer cobalt increases the durability of the carbide by keeping it from being so brittle.
The smaller the bit, the more it's necessary to make every part of the end mill count for cutting. Cheaper end mills have larger grains of carbide, while better tools have "ultra fine" grains. When larger grains of carbide are used in production, the cobalt has bigger gaps to fill between them, leaving you with a softer edge on your tool.
The best end mills are made with "submicron" grade carbide, which is what you want to look for when purchasing. It's more expensive to properly manufacture the submicron grade carbide, which increases the cost, but you'll be repaid with a tool that stays sharp longer, because there's less of the relatively softer cobalt involved.
Run-out Causes Premature Breakdown
Run-out occurs when the teeth of a cutting tool aren't precisely the same along the outside edges. Run-out can occur in two ways. Run-out can be axial, meaning each tooth along the end of the tool isn't uniformly resting on the workpiece, or it can be radial, meaning that each tooth along the outside of the bit isn't at precisely the same length from the center of the piece.
The corners of an end mill are its weakest part, making them prone to damage in the first place. Either type of run-out essentially causes some corners of the end mill to do more work than other corners, ultimately causing the tool to break down faster (or just outright break).
The biggest cause of run-off is probably overproduction without regard to solid (and expensive) quality control and individualized testing. When looking for good, quality tools, seek out a manufacturer that can clearly explain its process for avoiding problems with run-out, because it can be difficult to detect until you've ruined a few end mills.
Other factors that can cause additional cost are the geometry of a piece (requiring more complicated work to properly manufacturer it) and super-specialized coatings that are constantly being developed for micro tools in different industries. However, the cost difference between a good end mill and a not-so-good end mill may simply come down to the basics: better materials and more attention to production simply cost more to get.