If anything the early historical background is possibly the best part of 'Ontogeny and Phylogeny', especially in terms of the relevance of Haeckel and Von Baer to both modern embryology and evolutionary theory, particularly evo-devo.
The book is certainly still good, as in entertaining, informative and well written, but obviously what was then the most recent science is by now effectively historical as well.
Once you've read the book it might be good to look up some more recent work on heterochrony somewhere like
PubMedCentral.
TTFN,
WK