Even if it weren't considered a conflict of interest, there is a very intricate web of connections going on here.
Cookson had previously been on the board of the licence-holding company behind Team Sky. Cookson's son works for Team Sky. Given Sky's position in the sport and the potential for cronyism, if it hadn't been for the progress in respect of women's cycling under Cookson I'd almost have rooted for McQuaid to win the UCI presidential election, since it's better the devil you know. The web continues to a much more confused level between Sky and British Cycling though, much more than between the UCI and Sky. Does the man in the street know where the line between Team Sky and British Cycling is? Nearly everybody connected to cycling in the UK has some kind of relationship there; David Millar has the fact that British Cycling escaped the country's own embargo on dopers competing at the Olympics on his side and his close personal relationship with Dave Brailsford in addition to his sister's working for the team; the track team all have connections to the likes of Ellingworth and Brailsford, many of the women have the connection all the way back to the Halford's women's team that was built around Nicole Cooke's Olympic gold (which was of course done under the GB banner). The Sky sponsorship of much of the track team also helps interlink the athletes more (Chris Hoy and Victoria Pendleton have never raced the road professionally, but can still be seen in black and blue Sky kits), and the bonus interconnected web of the Murdoch press means that there is a very effective media blitz available to Team Sky (as we saw to a cringe-worthy level when the team first kicked off). This also means that dissenting voices can be buried under an avalanche of sycophantic drivel, which was the case even before David Walsh started wittering about symbolic yellow butterflies and damaging his own well-deserved reputation by producing arguments and cases unbecoming of a journalist of his standing in order to justify the team he was embedded at.
So, to sum up, Sky have connections on two levels to the head of the UCI, they are tied inseparably to the national federation that nominated that man to run for election to the head of the UCI, they control the public image of cycling in the UK, they have a strong tie to the media and a strong interest in quelling dissenting voices, and they have no problem with bending or hiding the truth in order to preserve their positions.
There is no evidence of wrongdoing on the part of either Cookson, Brailsford, Millar, Walsh or anybody else in the construction of this network of interconnected entities. But the system is clearly open to certain abuses, and such a network does maximise the opportunity for such abuses of the system to take place, and you would normally anticipate that a company with such a tangled web of connections would need to be quite transparent about operations in order to negate suspicions of actions such as, say, insider trading. And then we're coming back to asking for transparency out of Team Sky, and we know where that ends up.