The lesser-of-two-evils system can be changed if we move to publicly funded campaigns and take dark money and super-PACs out of the process. That would make it much easier for third party, non-party, or political minorities within parties to run and be successful.
There is a problem, known as "first past the post", also known as "winner take all". In a system where any position is held by the candidate that obtained the most votes in a poll, while everybody else gets nothing, even if they lost by a single vote, there is no incentive or reason to have a third party. With two strong incumbents, launching a third party requires a lot of money and publicity you probably can't have without tons of money to run ads- so essentially, the only successful third-party candidates would be Trumps. And if you just set a spending limit, even coming from their own pockets, then people will continue to vote R/D everywhere because that's the way it's always been and they are the only ones on TV after all. Look at the UK, where their "third parties*" only add up to 10 seats in a 650-strong Parliament, because people just vote Conservative or Labour, despite having tight and low expense limits.
The problem is the electoral system. Unless you change it, you are going to have a two-party system eternally. Because if another conservative or left-wing party arises and becomes successful, everybody will leave the R/Ds and join them instead, because otherwise you are just splitting up the vote and handling a plurality win to "the other side". In the UK, everyone who used to vote Liberal now votes Labour, after the Liberals were overtaken by them in the 1920s. After all, it's the only way to stop a Conservative Government from happening!
*not counting the SNP, who are essentially the one-party-state owners of Scotland.
I don't think a progressive agenda can really happen with the system we have now so, no, I don't agree that it would be a lot easier with Clinton over Trump. Maybe a tiny bit easier because as a Democrat she would have to pay lip service at least, but that won't really get things anywhere.
I don't think you are looking at this the right way. Having Clinton will probably mean a couple of steps ahead and, at absolu-horri-catastrophically worst, a "lip service" standstill. Having Trump will probably mean two steps back before even starting, and at worst, infinite steps back. Imagine: President Trump nominates a 40-year-old Scalia to replace Scalia, as the republicans want. Then, say, Justice Ginsburg dies and he nominates
another 40-year-old Scalia. And a heavy right-leaning SC decides to destroy unions (it's one of the pending cases on their desk), decide that people not elligible to vote don't count when approportioning representatives (favouring older and whiter states and taking a lot of EVs away from places with migrants like California or Florida; it's another case on their desk) or take on Roe vs Wade because hell why not, let us leave the matter to the states. All of that while wasting billions of money on the wall, starting political wars with all of their allies and reinvigorising the extreme nativist fringe. Suddenly, a progressive agenda is not just as hard to achieve as before, but actually much harder, because you first have to undo all the damage he's going to make.