It seems to me that the best cigar maufacturers, the ones with the most consistent, and best quality of cigars, i.e. Padron, Fuente, Perdomo, Torano, tend to be family (rather than corporate) owned, AND tend to be vertically integrated (or close to it). This means they have a major say in what's planted, how it's cured and processed, how the cigars are rolled, even what boxes are used, and how they're distributed and marketed.
ISOM's on the other hand have only recently fallen under the umbrella of Altadis. This happened at the end of 2000 when Altadis bought a large minority "holding" in Habanos (to the tune of $500M) and untimately used that to help start consolidating the cigar making processes in Cuba. IMHO, I expect that quality of Havanas to steadily improve over the next few years.