I don't put much weight to Alonso's comments. In the interview, he begins by being deliberately vague. And in fact, nowhere is he definitely specific. If Alonso stated that, for instance, that on such a such date Mercedes implimented a specific number of improvements, then it would sound believable. But instead he leads us to believe that "Every three or four races there is a little step in the engine". WTF?
As far as the situation that certain teams are "improving" their engines while others have not since the engine freeze... well, that's what F1 is all about. If some teams have found loopholes or some means to obtain more power than their competitors, then I have no problem with that. Ferrari are famous for seeking out and using such loopholes. And I stand up and applaud them for it. If a team makes it their policy to safely stand on the side of never pushing the rules, then they will be last on the grid.
Don't blame the teams, blame the FIA's vague rules and their enforcement methods.