This game was harder than the original G/S because of the much better moves and AI to throw a twig in the rotating bike wheels of experience. I agree that Totodile is probably the best choice, as he has access to ice moves and good old crunch making him a good all-rounder. I chose Cyndaquil and regretted doing so, to me he was just a fire type pokemon, and had a very limited movepool.
Falkner was a lot harder than expected, but was still quite easy, since i had a Geodude with Rock Throw. His roost annoyed me though.
Bugsy was quite difficult, and quite surprising to the 1HKO he was in GS. His Scyther was just painful. He wasn't too difficult though because of my strengths against bugs.
Whitney was surprisingly easy since i got the machop, Miltank lived up to its namesake as always, no matter what way you look at it.
Morty was quite a challenge once his Gengar came into play, as it immediately KO'ed the Haunter i had used against his previous pokemon. The addition of Sucker Punch was interesting, and made him much harder than before, although still open to Hypnosis.
Chuck was painful, He immediately took down my Pidgeotto with Poliwrath (after having his primape tossed aside), then it took the combined effort of all the others to take poliwrath down, although Haunter did a lot of the work.
Jasmine was no harder than in GS, but was still an obstacle because of that monstrous Steelix. Despite my elemental strengths against Steel, its defense made it a nightmare.
Pryce was easier than in GS, which i didn't know was possible.
Clair was surprisingly easy, but thats probably because i prepared more against dragons than in GS, but her Kingdra was still quite a pain.
The E4 were dissapointing, apart from Bruno who was surprisingly difficult than before. Will was much easier compared to GS, but that might be once again due to me being more prepared against him.
Kanto had a great 'not too tough, not too easy' feeling to it, which suited it being a further challenge as well a suitable drop after you become the pokemon champion. Blue was a decent challenge though, mostly because Bulbapedia lied about what his first pokemon was.