I just want to record here a few things I've learned lately concerning the motivational question about the empirical linearity of "plausible" theories of arithmetic.
This empirical fact -- that all "plausible" theories of (first-order -- or even second-order) arithmetic appear to be linearly ordered by their direct implications -- seems to be a pretty famous fact among logicians. I recently came across some further discussion of it in Woodin's Notices article.
To see why one might expect this, one can contemplate the $\omega$-rule, i.e. the (infinitary) deduction rule which says that if you can deduce $\phi(n)$ for all numerals $n$, then you can deduce $\forall x(\phi(x))$ (where we work in the language of first-order arithmetic). It's easy to show that when first-order logic is augmented with the $\omega$-rule, the axioms of $PA$ (or even $Q$) generate a complete theory (though I found it surprisingly hard to find a source bothering to both (i) spell out what the $\omega$-rule is and (ii) explicitly state that it leads to $PA$ being complete!), and that indeed this theory coincides with true arithmetic. Therefore any theory of arithmetic which strengthens $PA$ (or even $Q$) and which is not just a weakening of true arithmatic must prove, for some formula $\phi(x)$, every instance $\phi(n)$ for numerals $n$, while also proving $\exists x (\neg \phi(x))$ -- a situation which sounds pretty "implausible"! This suggests that every "plausible" theory of arithmetic must be true arithmetic or a weakening thereof.
Of course, this argument requires our metatheory to reassure us that there is a complete theory of "true arithmetic". I'm no expert, but the only way out I can see to entertain the possibility of truly "plausible" alternate theories of arithmetic to exist is if one changes one's metatheoretical assumptions. It seems to me that as long as one assumes classical logic in the metatheory, one has to concede that there is a complete theory of true arithmetic, and I don't see anywhere where choice is used showing that the $\omega$-rule completes $PA$. So even if the metatheory is $ZF$, I think one will still be led to the conclusion that only true arithmetic is "plausible". Probably, then, one needs to weaken at least to an intuitionistic metatheory in order to contemplate the possibility of "plausible" alternatives in the theory of arithmetic.