For the principle of checks and balances to work effectively in the way you're thinking, you need the different actors to check each other and to affirm one another's authority, with an intensity commensurate with any excesses attempted by any of the branches, and proactively.

Right now, Congress isn't doing much to encourage good behavior, and the limited resistance from the judiciary is more likely to undermine the courts' standing in the eyes of the public than to constitute a meaningful and lasting check on the Trump administration. The outcome will be that the administration will push right up against the farthest limits of its authority, possibly pushing those boundaries farther back than intended or ideal, either in general or in specific matters, with long-lasting consequences (eg. the harm done to US-Muslim relations as a consequence of the immigration order). It's a risky state of affairs.