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Do you think that there is a better way to produce vaccines?

Technically, there are probably better ways to produce flu vaccines. The use of chicken eggs is problematic for a number of reasons. For example, it is inefficient, producing only one dose of vaccine per egg. Each virus strain contained in the final vaccine is a separate dose, so that vaccine cost the lives of three or four baby chickens (not that anyone really cares about them). Another issue is that the vaccine viruses have to be adapted to growth in chicken embryos, which means that they may not match up completely to the circulating viruses that are adapted to growth in humans.

A few years ago, a company got FDA approval to sell an influenza vaccine grown in mammalian cells, actually dog kidney cells. (Immortalized cell lines, they are not killing dogs to make vaccines!) This has the advantage that it is more efficient, and the vaccine viruses are mammal-adapted, which means they more closely match the wild viruses. Other strategies to produce vaccine include various synthetic methods--that is, a piece of DNA that codes for artificial proteins that contain antigenic portions of influenza proteins is made and used to make vaccine, either by completely synthesizing it in a cell-free system or putting it into mammalian cells which then become little vaccine factories. There are many efforts underway to find better, more efficient ways to produce higher quality vaccines.

The problem with this year's vaccine is the variability of the influenza virus itself, that I mentioned in my previous post. The WHO influenza experts use data on strains that are circulating in one hemisphere to try to forecast which strains will predominate when flu season hits in the other hemisphere. (Thus, they are meeting now or have already met to decide next year's strains for the southern hemisphere.) As you might guess, this is a bit more challenging than trying to forecast the weather a few days out. Any given strain of influenza only circulates for a few years, until the point at which most of the population is immune to it. Then it mutates so that it can avoid all of that immunity, and people are susceptible to it again. We also say that it is a different virus at that point. This is an on-going challenge, which we cannot ever really overcome. This is why so many researchers are going after the "holy grail" of influenza research--the universal vaccine. Which may be impossible to achieve.

I should point out that in the thread you linked, the article said that 80% of the influenza cases this season are of the H3N2 strain. The vaccine was only 10% effective against H3N2. These two little facts suggest to me that the vaccine was actually quite effective against the other two or three strains included in the formulation. I'll say that my own impression, with the number of people calling in sick, is that there is an especially high number of cases this year. I don't know, though, since I have not done any kind of formal study into the incidence of influenza this year. I haven't had to be the resident flu guru at work for a couple of years now... no, I'm not being facetious--two years ago, knowing everything about influenza was my primary job duty.