Well, that's still right, whether there are same-ish fundamental particles or not.
Just a pair of particles being the same in all their aspects doesn't make them identical. For example they don't occupy the same place in space.
Of course there are not two identical things in the universe. Because being identical they're the same thing, aren't they? It's called the identity of indiscernibles. https://en.wikipedia.org/wiki/Identity_of_indiscernibles
And one may disagree with the "unmoved mover" (let's call it an) axiom but if one takes that as given then it is plain to see that Leibniz's argument holds. And say you actually do disagree with it as an axiom then you have a bigger problem, what Umberto Eco called the most intractable problem of all, the problem that generates all other problems, namely, "Why is there something rather than nothing?"
Eliezer Yudkowsky has made an argument against doing epistemology by intuition [1]. Famously, Henri Bergson tried to use his intuition about time to dismiss special relativity, and while he may have swayed the Nobel prize committee [2], his ideas were swept away by history.
Turning now to your last paragraph, it is like saying Bernie Madoff's clients were wealthy because the arithmetic in their statements was correct. Also, one cannot validly argue against the rejection of a self-serving axiom on the grounds that doing so leaves problems unsolved.
[1] http://lesswrong.com/lw/q1/bells_theorem_no_epr_reality/
[2] http://nautil.us/issue/35/boundaries/this-philosopher-helped...
http://lesswrong.com/lw/ph/can_you_prove_two_particles_are_i...
Logic, science and philosophy (and Leibniz did all three) doesn't concern itself with the "common understandings of the world".
In the Leibniz's example, he wanted to set first principles -- that go deeper than the "common understanding".
Just a pair of particles being the same in all their aspects doesn't make them identical. For example they don't occupy the same place in space.
From the accepted answer:
That's what a Bose-Einstein condensate is: lots of bosons in the same place and quantum state.