The 4th gen mechanics have caused a severe altering of everything you ever knew about the ingame Pokemon. Aside from ones that are now showing up ingame for the first time, certain monsters are now suddenly usable - or no longer usable. The major culprits for this of course, are 4th gen mechanics and the sudden lack of elemental punch TMs, as you'll see...
I'm pretty sure Gyarados is the first Pokemon in the history to be promoted from HM mule status. Back in GSC, all the Red Gyarados did was take up a slot in my party between New Bark and Victory Road for the water HMs because there were a lot of good Water types on the special end of the spectrum. It's now a lot easier to use a physical Water-type and even then, you can use it for Surf as its SA is now "meh" instead of laughable. Plus, it can be soft-reset for stats and nature.
2) The collective Safari Zone Pokemon
There were about 20 Pokemon that couldn't be obtained in the originals before Kanto, and most of them are now available much earlier in the game. This includes Jigglypuff, Clefairy, Murkrow, Misdreavus (also available outside if tearing your hair out doesn't appeal to you), Kangaskhan, Cubone, Marowak, Lapras on days beside Friday, and my new favourite - Larvitar. At the very least, you can use a non-Geodude Rock-type for a while - and having something with Sandstream helps big time when the final boss has auto-Hail and three things with Blizzard including a Lapras.
This was a 3rd gen benefit, but still... 98% accurate Sleep Powder. Soul Silver players are SO screwed. I know I mentioned getting Butterfree is a pain before, but you did the same thing in RBY right?
Now that Tangela can evolve, Tangrowth has become the best ingame Grass-type and anti-Water device since the stones are STILL rare as heck unless you spend half your time in the Pokethlon.
5) Spearow and Hoothoot
Spearow has Aerial Ace prior to evolution and confirms that anyone who uses the Pidgey line needs to submit to drug testing. Hoothoot now has Air Slash and Uproar to actually be usable (lay off the Hypnosis, though).
1) Kadabra and Alakazam
Oh, how the greatest ingame monster has fallen. And it was set up so well, considering if they crossed the Game Corner of HG/SS with the original's department store, you'd win the game with $11k. But the major thing is that instead of type coverage that would make Mew reconsider its position in life, you're stuck with Psychic move/Focus Blast. Not really that fun, is it?
2) Mareep family
Unfortunately, Mareep has gone from "powerful team member" to "ingame fodder". The big problem? No Fire Punch gives him type coverage of Electric, Electric and more Electric until it gets to Ampharos. By which point, you've punted it for something with actual variety in its learnset. Signal Beam and Power Gem are just plain teases.
3) Houndour, Sneasel, Electabuzz, Porygon
Or "the four families that don't appear in Johto for some stupid reason". Surely Houndour could appear on, say, Route 37 at night in place of Fire-type du jour? Or would that have made the Ghost gym too easy? Sneasel suddenly becomes passable in the 4th generation, and it was in the Ice Path in Crystal, so why leave it out? Electabuzz has a baby form, so you would think it would be available and why can't the Goldenrod Game Corner borrow a few Porygon to sell at a discount?