They're nominated by the president, but approved by the Senate. There have been cases throughout history where a nominated judge doesn't get through the approval process. Of course when the president and the Senate are aligned and in agreement this approval process is largely a rubber stamp.

Can't he override everything with pardons and executive orders anyway?

Not at all. Despite what it sometimes looks like, the president's executive order powers are quite limited. But again, if congress isn't willing to challenge the order and the Supreme Court isn't willing to rule on it, these limits are more theoretical.

Can't the US constitution be, uh, amended?

It can, but it is a slow and difficult process, requiring 2/3 support of both the house and the senate, plus support from 3/4 of the States. There have apparently been over 10000 attempts to amend the constitution since the founding, of which 27 have passed. Furthermore the president has no power to suggest or approve constitutional amendments.

Basically a president that doesn't have the support of Congress and the Supreme Court has surprisingly little power.