There are a couple examples I'm aware of where choosing to axiomatize $\mathsf{ZF(C)}$ using collection instead of replacement results in a much nicer (or at least less surprising) picture:
Let $\mathsf{ZFC}-$ and $\mathsf{ZFC}^-$ be "$\mathsf{ZFC}$-without-powerset" presented using replacement and collection respectively. Then $\mathsf{ZFC}-$ is weak in a number of annoying ways, while $\mathsf{ZFC}^-$ behaves "as it should;" see Gitman/Hamkins/Johnstone.
Parallel to the above, let $\mathsf{ZF}\ominus$ and $\mathsf{ZF}^\ominus$ be "$\mathsf{ZF}$-without-extensionality" presented using replacement and collection respectively. Then $\mathsf{ZF}^\ominus$ is equiconsistent with $\mathsf{ZF}$, while $\mathsf{ZF}\ominus$ is all the way down at the level of $\mathsf{Z}$. These facts were proved respectively by H. Friedman and Scott (see this old answer of Andres Caicedo). While low consistency strength is in one sense a tameness property, its appearance here is quite surprising (to me at least).
Overall, these results suggest to me that collection rather than replacement makes more sense in terms of presenting various set theories.
Are there notable exceptions to this theme - that is, situations where using replacement rather than collection results in a "tamer" picture in some sense?