Then what interest would small states have in joining a federation? In my view, a 'federation' implies equality between the states comprising it, and the voting rights of the citizens of the bigger states suffer a dilution, which is the price of joining the union.

Will it be acceptable to the member states of the EU, any configuration that makes some members more equal than others?

Also in countries like India, this could offer a perverse incentive for states to refrain from population control policies.

Also some states having larger populations than others is a historical accident.

There are 500 million members to the EU. I am in favor of all of them being equal, yes. We still have to quelch local nationalisms so there are some compromises being made to give state some kind of sovereignty, like the US used to need 200 years ago, but once the reasons for these are removed, remove these privileges.

India: You assume states work against each other and populations automatically favor their states over the federation they belong to. If that's the case, you have a cultural problem to solve first. I doubt this is the case in the US right now.

And yes, there are various reasons for some state to be populous. It is irrelevant with the question on whether all the peoples' vote should have equal weight.