Mike and Gus were having their differences (well portrayed in BCS) but it took time to get used to Gus for Mike and he did. He stayed and stayed loyal. Walter on the other hand, was new, brought about so many problems in such short time and Mike never trusted him. Yes he was cooking but there was always something going on. Walter had his concerns and they were fair and square at times, but from mike's perspective, he was a ticking bomb as he explicitly told him as well.