Suppose I have two outputs A and B, each with a value of 0.5 BTC. Presently there is no information in the blockchain that indicates A and B are owned by the same person. If I want to send 0.75 BTC to a third party, I must create a transaction that takes A and B as inputs and creates a 0.75 output C and a 0.25 change output D.
An attacker looking at this transaction can conclude that the same person owns A, B and, D because it would not have been necessary to combine A and B if the real spend was only 0.25. It would not matter at all if A and B had been mixed prior to this operation or not.
You are quite right, A, B and D are associated at this point in your situation. Of course, with an M-to-N mixer, A and B could have been combined together into say E previously and then E could not have been linked quite as easily to C or D, as it would be unknown which of them is the payment and which is the change. The same result can be obtained however by mixing N-to-N twice, a first time with A and B to unlink them and a second time with D after the transaction you were proposing. In such a way, the outputs of A and B (which we can call F and G) are linked to spend C and change D as before, but since neither F, G, C or D are linked to anything else after the second mixing, who cares?
Now you are right that my approach takes two mixings while yours takes only one but it is actually more secure since D cannot be linked at all to any other of Alice's future transactions as it is mixed right after. In your approach, an adversary actually would have a 1 out of 2 chance of correctly guessing the change address anyways, whereas this probability of guessing is much smaller in the case of a secure mixing.
you have to combine smaller outputs from time to time in transactions
Yep, that's just the point of mixing these small outputs. After the mixing, you can just throw them all together in one large output if that is more intuitive, but you can actually go straight to spending them together in one or many larger transactions without caring if they are linked together, as they are linked to nothing else.