Small quantities of food on KLM
I don't think what they offered complimentary was out of order for the length of flights you undertook, unfortunately KLM catering department cannot know everyone's schedules and offer each differing passenger meal base on this. They have to base it on the actual flight as the majority of people it will be their only flight with the airline that day. There is no point Going overboard and offering a three course meal that no one eats. why this is being used as an example of bad customer service I am not sure.
You say that there was no or very little in the way of business class signage for check in, yet there was a queue you had to join at the economy line, enough people obviously found the correct line so it must of existed somewhere, yes it could be bigger or more clear but it must of been there somewhere for everyone else to find. Also the fact they filtered the economy customers to the business class check in as and when they could between biz class
Customers shows good customer service, they could of made you wait even longer and just kept the lines separate.
Case sizes? That will always cause issues on smaller aircraft but the staff asked you for a reason, it maybe that you wheelie case was not the type that could be squeezed on due to the bottom wheel design but the persons bigger rucksack next to could be squashed under the seat or in the locker. That is not bad customer service, that is being honest.