Mixin with a count greater than 1 needs also the breaking out of transactions into powers of 10 down the the lowest level of precision used. So for example 0.00012959874 gets broken down into 0.00010000000, 0.00002000000, 0.00000900000, 0.00000050000, 0.00000009000, 0.00000000800, 0.00000000070, and 0.00000000004. Otherwise these remainder amounts are unique and cannot be mixed. Furthermore for this to work this change needs to be implemented ahead of the mixin change to provide enough transactions in the blockchain for the actual mixing to work. This needs to be addressed at the protocol level.
Right now anything with more than 2 decimal places cannot be mixed with a mixin over 1 and this is the cause of these problems. Asking exchanges to use higher mixin levels is doomed to failure without addressing this mantissa issue at the protocol level.
just a quick idea (dunno if it is stupid), if merchants (exchanges) wont adopt it, from my understanding, you could just send the 1 mixin funds to your wallet and resend it with a mixin greater then 1, to another address you own, right?
perhaps this can be done automatically, like generating an address in your wallet which you could mark as an "unclean" receiving address, and your wallet will automatically resend funds recieved to that address to another one of your addresses with a mixin greater then 1.