You could get Sneasel earlier in Crystal, and Misdreavus earlier in HGSS, yeah.
And, I definitely agree on Spiritomb and Munchlax or even Feebas in Gen III/IV; and I think that honey trees are effectively an even worse incarnation of headbutting, but with a timer on it now, too.>Isn't that what all Pokemon catching is? Just run around somewhere and pray you get the right encounter?
I'd argue you have a little more control over what you encounter in conventional catching. You know that if you go to a specific route, you'll encounter a certain set of Pokemon - but the way GSC handled trees were that some would have a smaller selection (no Heracross, etc) and general encounter chance overall -
and this is compounded by the fact that the Pokemon exclusive to this have such a low encounter rate overall; so you might be deceived into thinking 'oh, this is the wrong tree' when you run into 20 Spearow when it was just RNG dicking you over. HGSS rectified this, though.
I agree on your other points, though - GSC did a lot better at rewarding exploration and didn't have anywhere near the level of tedium that DP, and to a lesser extent Platinum, had.