Trapinch, Vibrava, and Flygon all should've been Bug/Ground.
Vibrava and Flygon would still have Levitate, of course, but no Dragon type... they're even less dragon-y than most other Dragon-type Pokémon are. And that's saying a lot considering that
Altaria (aka "HEY LOOK, I'M A BIRD! Yep, a bird surrounded in clouds. Couldn't possibly be anything else! I mean, just look at me--beak, talons, feathers, wings... BIRD!") is one of them.
Speaking of Altaria... Normal/Flying would make a lot more sense (and poof, no more double-weakness to Ice! Why would something that lives in the clouds be so vulnerable to Ice anyway? It's usually
colder up there than it is at ground level!)
Staryu should probably be Water/Psychic... never really made sense how Starmie was part-Psychic but Staryu wasn't, even though Starmie really isn't any more "psychic-ish" than Staryu...
Azurill being Normal instead of Water seems a little odd, too... it can't be
that much worse at swimming than a "needs its tail-ball-thing just to stay afloat" Marill, can it?
Rayquaza could have easily been the first pure-Flying type, if only they had made it look like something other than a dragon...
Not sure why Jirachi is part Steel-type... though I can't really think of anything else it could be besides plain old Psychic.
No idea why Lucario is part-Steel, either... I see nothing metallic about it at all (and I'm assuming those white spikes on its hands are intended to be made of bone, otherwise Lucario learning Bone Rush makes no sense.)
Same goes with Palkia's Water type. I know Water/Dragon only has one weakness, but that can't possibly be the only reason they chose those two types together for it (at least I really hope it isn't the only reason)... I just can't figure out what the real reason is.
And Drapion shouldn't have randomly lost its Bug type in favor of [SUPER GENERIC PSYCHIC-IMMUNITY TYPE]. It's still just as buggy even after evolving, after all. If they had just made bugs immune to Psychic instead of tacking on an extra type, we wouldn't have had this problem...
The Gastly line is part poison because in RBY no type was super-effective against ghost
This is 100% false. Ghost is super-effective against Ghost, and always has been, even back in R/B/Y. Go over to the tower in Lavender Town and use Lick (the only regular damaging Ghost attack back then) on a Gastly, if you need proof. And on top of that weakness, the R/B/Y ghosts all have low physical defenses, so even if they weren't part Poison they'd still get hit pretty hard by Ground, Rock, and Flying moves.
The R/B/Y ghosts (especially Gastly) are part Poison because they're made up of poison gas that can choke you if they float around your head.