The villain wasn't that great..

The real villain here was Time and the screwed up nature of the world. Logan had been battling its many faces for a long time and the message was made clear that even he couldn't win. Sure we all have our good days, but there is no permanent happy ending even for the best of us. Look at how Prof X's life work ended up. It was almost like the longer Logan lived, the more familiar he became with this faceless foe. Time and Logan knew the endgame and Time didn't rub victory in our faces. It seemed fitting to me that Pierce and Dr. Rice weren't the main focus as they were merely puppets. Their deaths weren't even really climactic. I think Gollum echoed the point well in a riddle:

This thing all things devours;
Birds, beasts, trees, flowers;
Gnaws iron, bites steel;
Grinds hard stones to meal;
Slays king, ruins town,
And beats mountain down.

Yeah, I don't think there was supposed to be a super duper "better than ever" villain. In fact, why even try to En Sabah Nur?

As Dan sez, it was pretty much about Logan and Charles, and time. Also, without the mention of everyone else (most conspicuously Magneto), I think this film was supposed to stand more or less apart from the general X-men timelines.

I haven't EVEN been out to the wikis yet to see how badly this film horks up their various timelines, where it fits in the re-imagings,canon, etc. It's really all quite a mess in that regard.

So to me, it was really not just apart AND alone, but pretty much only related to the X-Men universe at large in the respect that it helped if you knew just a wee bit about the mutant history, the school that the old man use to run, what the heck was going on with the blades those two had coming out of their knuckles ... but you could still probably enjoy the film with only a rudimentary impression of all of that.

A huge villain probably would have detracted from the story they wanted to tell.

I agree, and I think the doctor fella was weak as well. Assuming you were talking about gold tooth cyborg fella. But Xavier and Logan, damn. They were good.