What do I not want to see?
Honey Trees: Nice idea, honestly, but not the best execution. Making it timed was pretty horrible if you wound up forgetting about playing the game for a day.
Exclusives in Bug Catching Contest: Yeah, there's no need for it. You've already got exclusive bugs (Spinarak and Ledyba), so unless there's newer ones from 3rd or 4th gen, I wouldn't bother with making any exclusive. Maybe make one more common than the other (Pinsir in one version, Scyther in the other)? That'd be fine with me.
Low Level Leaders and E4: What can I say? First time through Silver and Crystal, they were okay. Second time through? Not nearly as hard.
Pokemon from RSE or DPPt: Not until the national 'dex is gained, anyway. Same goes for legendaries from FR/LG.
Apricorn deletion: I could see them making the Apricorns a required component of DPPt pokeballs, and you'd have to go out and collect them in order to give them to that guy who made the Apricorn balls. I figure that he'll either give you the balls for free or for a discount compared to higher prices for the ones sold in a pokemart.
Headbutt Tree deletion: Now, this I liked. I think that there should be a numerical limit per tree, per day, however (say, twice per tree per day) rather than being able to do it all day long. I dunno about you, but knocking down a dozen Weedle, half a dozen Aipom, and a couple of other bugs before coming up with a Heracross is just really weird- I'd expect the Heracross to get the heck outta there ASAP after a few headbutts, if it wasn't knocked out of the tree in the first place.
Move Tutor Inflation: Please, no more 200,000 poke-dollar TMs (dang casinos). Remember when the Move Tutor would teach 'em for 10,000 in Crystal? Granted, if there are more trainers, or at least if the monetary rewards go up, then the price can go up, but sheesh!
Starter following: Not unless there's a good reason, and making the game like Yellow is not a good reason. Maybe if they seek out rare pokemon in a route or something once a day? That might work and be worth it.