The imperial presidency started well before FDR. Some trace the socialist problem to Wilson, others to the other Roosevelt, some even to Lincoln. You are correct that by FDR it was certainly under way, and only committed socialist/communists deny it. If you are sticking strictly with "imperial" that goes back to at least Andrew Jackson who used the office to destroy the National Bank (perhaps a good thing, perhaps not) in defiance of Congress.
The drone issue is a mixed bag. If the American is in foreign territory and known to be helping the enemy, that is engaged in subversion against the US, I have no problem dropping a drone on him. The presumption of innocence only goes so far, and it's right out the window when war starts.
Presidents have ALWAYS had the power to suspend habeas corpus. Washington himself suspended it during the Whiskey Rebellion, which he put down with US troops. Moreover, this is an assertion of suspending habeus corpus for foreign agents, a claim I find specious at best. He isn't routinely suspending it for US citizens who aren't known to be acting as foreign agents.
The Constitution also allows for the creation of "other courts" which is essentially what the national security letter system is. It may be being used to liberally, but that is an issue separate from the authority of Congress to create such an alternate system.
I concur that executive orders have been used too much, and the example you site is particularly egregious. I will note however that progressives/socialists/communists have long been at work undermining that right and the courts have generally supported this. The history goes all the way back to Miller, a case that if a lower court today were to treat the defense the way SCOTUS treated the defense in Miller, the presiding judge would be subject to a STERN rebuke and even possibly disciplinary action from the Bar. Such is the way of dictators and their sycophants who will rule when a free people refuse to hold their government accountable. We failed miserably on that count in the last election.