I would agree with that. But actually, as far as I am concerned, they should just abandon the 'calculations' as they are now, and have a set maximum squad number for all qualifying nations, of say, 5. And the qualification should be decided simply on race results in all the major Pro-Tour and Continental races regardless of the status of the rider, as you suggest. Having different numbers in squads is ridiculous, if it is to be genuine international competition. The other alternative is simply to abandon the nationality element and make qualification based on individual riders' results. You'd get the 'best riders' but it would be even more skewed and you'd get de facto national squads anyway.
Er, maybe, but at pro level individual racing simply does not happen. Individual results only matter to a team in that the protected rider delivers, and domestiques ride themselves into the ground for that. So if they were measured individually, they might be less inclined to do so.
Whilst to represent your country might be an honour, it does not pay the bills and doing your job in a team does. Which would you choose?
On the system, it does skew representation unreasonably, as most of the best GB riders are in ProTour squads (as they should be), it means only ProTour races count for ranking points, and Sky (for instance) have hardly had an outstanding season. Thus are some of the best countries disadvantaged against nations who only operate at continental level, where the points gained there count. So we have three GB riders and six (with all due respect) lower quality Iranians in the biggest one-day race. How daft is that.
The solution which seems might work is to simply divide the number of nations entering into 200 (field size maximum). Thus if 32 countries want to ride it would be six riders each, plus a space for the current champion, 193 riders. Does this seem sensible? If the countries entering HAD to have ProContinental or Pro Teams registered (say a minimum of 3) then the numbers would work. Even 40 countries would get 5 riders each (plus one (not counted) for current chanpion, so 201 absolute top. Look back and see how many countries ride, just look at the convoy. Even then snmaller teams lose out, as those with 9 riders go in the first draw, 6 riders in the second draw, others in the third draw. So GB will probably be car 29 or some other useless place.
The whole system needs a proper review, but then UCI has never worried about skewing the rules when it suits!