I also think there is too many monsters IF they are too be seen as regular species from the campaign world's ecology. For that reason, I restrict the regular species to a limited number, mostly animals. Then, all other monsters are occasional exceptions. Some examples:
- Except for animated skeletons and zombies, there is no clearly defined types of undead that exist in the world. Rather, undead traits are almost random, and for that I use whatever undead critter I can find in the MM (or stat myself). If there are many wraiths in one place, it probably because one created many more, but it's not a specie of undead in itself.
- Giants come from Jotunheim through overlaps with the material plane, that occur in some places and specific times. Sometimes a giant or two could become stranded in the PC's homeworld, but usually they return to Jotunheim when the planar overlap ceases.
- Things like a mimic or ropper may be living things, but they are definitely not species. They are unique beings created by some magic-user or supernatural event. They will be found once, maybe twice, but are otherwise unknown and never encountered outside of the single dungeons where the PCs adventured.
- Most aberration creatures aren't species, but mutations of normal creatures due to magical pollution. Well, one or two (such as the owlbear) have been known to reproduce, but even in their case aren't found worldwie (only a few specien in a specific region).