>>41398705I think they worked better because when they were these mysterious and optional encounters which you could completely miss, rather than being intregal to the plot (except in the case of Suicune). It's also why I find the Regi trio so memorable. I don't quite how to explain it, but these pokemon are supposed to be figures of myth and legend. You hear about them in rumours, no one is really certain if they're real or not, then when you eventually out that they are real, that's what makes them special.
When you just shove them into the main story through mandatory encounters, it removes that mysticism and uncertainty which makes them special in the first place.