After reading over most of these, here are my improvements.
1) Visible day / night return, though without such special times to catch pokemon - 10% of catching something in the twilight hours upset me.
2) A new type, as long as it is balanced (I don't care what it is called) but it should be weak to Poison. Everyone has to agree that there is no way poison is the strongest type, and many would say it is one of the weakest (despite some of the pokemon having excellent stats, ex: Weezing's defense and Drapion's attack)
3) The "haze" weather type (or whatever name you want) for poison sounds good, along with other weather effects. I really enjoyed when they added in the effect for sandstorm for rock types
4) More double battles added into the game - increasing two of your pokemon's EXP is always a benefit, and it is much more strategic than a single battle without a doubt
5) Bring back the "Fast" surf - The one from leaf green/fire Red
6) Keep the fast bike - I don't know if anyone ever tried to hatch eggs in leaf green / fire red, but it was horrible
7) More box space - I've released about 400 pokemon from my Diamond game and it's just plain annoying
8) Bring back the Item Storage, Though don't make a limit on how many items I can have in the bag - Having 50 fire stones from the underground in my bag is not necessary
9) Get rid of the special events and all that, though of course they wont, just throwing it out there
10) The DS is far enough advanced that you can have the pixelated pokemon go over and "punch" the other pokemon, it wouldn't be that hard
11) Throw in some random weather. It would make the battles much more interesting.
12) Flying. Everyone has this type because it doesn't get hit by earthquake, but besides that, what's the use? Drill Peck is between aerial ace and brave bird, but only like 3 things can learn it. Expand it or put another move in there (when Air cutter and Air slash were designated special it made me sad)
13) A rock type with special defense instead of defense. What a miracle that would be.
14) An evolution for Farfetch'd - I recommend Far'awesome, obtained by trading with a awesome sash.
15) You have Vileplume. You have Victreebel. They are almost exactly the exact same pokemon with the exact same moveset. Change that up.
16) Bring back the telephone, but don't have anyone call you besides the important characters. Reading "Hey Charles, today I almost caught a weedle, but then it got away. I'm getting a feeling I'm not too good at this. Talk to you later!" gets boring after a while.
17) Get rid of magikarp trainers. The worst thing in the world is when you have to watch 6 magikarps do splash attacks.
18) Go back to the original fishing - I don't want to press "A" when the dots appear correctly
19) I don't know who decided there should be a dark eevee before the original ones got satisfied (rock, poison) but come on.
20) How many pure steel types are there? Mawile? Two things on that. Add more of those, and give mawile an evolution.
21) Who thought that making "Screech" an 85% accurate move was necessary? Is it that much better than Fake Tears? Certainely not.
22) Increase the power of both "Pursuit" and "Feint", they are moves that take foresight and skill and should therefore be more appropriate.
23) Gunk Shot. Very necessary poison move. Why is it only 70% accurate? You can not consider it as good as Blizzard, especially in double battles where Blizzard hits both (Gunk shot comes with only 5 pp as well...)
24) Why did they take Pay-Day away from Persian? Was it just too good a move?
25) How about a potion in between super and hyper (that isn't a soda you have to go out of your way for)
26) Buy max revives. Yea, you can do it by buying it by a different name, so why shouldn't you be able to buy them by their normal names. Oh yea, it takes away your pokemon's happiness when you use it. That's a large concern right?
27) Remember in, I think it was leaf green / fire red where you could battle a trainer a day? That was fun. Or the battle towers from Emerald? Those were fun. Even the battle tower from Leaf Green / Fire red was entertaining. But there was no need to "downgrade" them in the new game - Oh, I can team up with a computer who has a fearow who is consistently using agility? What a deal. Fun time.
28) Even if you were to keep the battle tower from pearl/diamond, why do you have a "champion trainer" for the single battles and not the double battles? Why are those more desirable?
29) Can my rival not constantly run into my ass?
30) How about, no champion. There is no champion. Just make the elite four slightly harder and don't have a champion at the end.
31) I want a bug / flying that isn't the exact same as Butterfree. Beautifly is the exact same thing. And why did Surskit change from a bug/water to a bug/flying when he evolved - why can't we have a bug/water? And why isn't the bug type resistant to either dark or psychic? No matter how good my bugs attack/sp. atk is, the psychic type is usually faster, and a good psychic takes me down.
32) Why doesn't Kangaskhan have a baby? It clearly does in its pouch.
33) A physical ground move between magnitude and earthquake (exclude bonemerang and boneclub, they are specialty moves). Nobody uses dig. I'm sick of every ground type in my double battles having to go out with a flying/levitating/grass type to be of any use
34) If there is going to be a new HM, make me want to have it. Defog/Rock Climb/Rock Smash are jokes.
35) So Hypnosis can put a dark type to sleep even though it is a psychic type move, yet Thunder wave doesn't affect ground types? Why?
36) I want a fighting type with defenses.
37) Stop this massive dragon power splurge. Dragonites 134 base attack combined with it's moveset, type, and speed, makes it unfair. They made Altaria, continue on that path. Make them even. Then you could even have dragon types not four times weak to Ice (Excluding the legendaries of course...)
38) Customizing your character's wadrobe/looks, and even perhaps their "catch phrase" that they say when they beat a trainer.
39) I beat the elite four, why don't I get to stand at the end and wait for new challengers? I am the champion aren't I?
40) More efficent yet informational information in the "attack descriptions" during the game - be more like psypokes - say "Headbutt: Uses the head to strike a blow with a 30% chance of flinching." Isn't that the useful information we need?
41) Running shoes at the beginning - I just got done playing Fire Red and it was horrible waiting until I beat Brock.
42) Remember when you beat leaf green / fire red how the Elite four's pokemon went up to level 70 ? That was amazing for leveling up your guys. Do that again.
43) Banette. It learns all "use" moves (Snatch, Switcheroo, etc) and then has no defenses and all attack, yet it doesn't learn a single ghost type physical attack (yea you can TM shadow claw, but then what?)
44) I'm not a big pokeball seal user, but why should you have to take the seal off when you put it in the box?
45) So. We have the "splash" move, which I find hilariously entertaining. But who decided it was necessary to make it incapable of being used during gravity? Was that really necessary? Like honestly.
46) I'm sick of fire/grass/water starter every time. How about choosing from a rock/flying/poison starter for once? Give the underused types some powerful pokemon to back them. No matter what, enough fire/fighting starters (though I am of course a fan of Blaziken and Infernape)
47) Let me know if I'm supposed to sell an item I pick up in the description. "A shiny piece of crystal that glitters pleasantly in the sunlight" does not tell me if I should attach it to a pokemon to increase their beauty stat in a contest or if it is worth 200 pokedollars.
48) How about a ghost that has arena trap/shadow tag so that curse/nightmare can have more of a use
49) At the end of the game can someone not say "You still enjoy the enthusiasm kids bring to your research don't you...", because that's just creepy.
50) I don't want the evil villain to turn good in the end. Give me a good "Giovanni" type character again with an actual evil personality.
51) Put a PC in the starting town so you don't have to carry a "flyer" with you every time you beat the Elite 4. My Level 14 Staravia has been through the elite four more than anyone else in my box, just to fly me back to the elite four...
52) Can something that isn't a water type learn water sport? Same for the groundtypes learning mud sport?
53) Can something slow learn agility?
54) A great addition was letting me know when my quick claw took effect, but why can't it signal me when my razor claw/razor fang, etc, take effect?
55) The possibility to turn on an "auto-save" feature - If you don't save every 45 minutes/60 minutes/etc it would do it for you. Remember the lsat time your little brother came over and turned off your DS, or you accidently hit the cartridge out of the top? It sucks.
56) Legendaries don't need those amazing moves/abilities (Bad Dreams), pokemon like Farfetch'd and Ariados do.
57) Remember that incredibly hard psychic gym in Emerald with the double battling twins? Remember how much glee you got when you beat it? That's how they should always be, difficult - they are gym leaders...Gym leaders like Brock who have a geodude and an onix with bide should be extinct by now.
58) There were two poison types added to the new game (not even pure poison, poison/darks, which I do like the type by the way, but still), and there was only two fire types added to the new game (the starter and magmortar) to my knowledge (not including legendaries). More even distribution of new type pokemon pleaseeeeeee (That means that only 8 out of 93 pokemon, that's not including the legendaries, were either poison or fire types. There should be an average of 7 per type if that 93 was properly divided)
59) How about an always functioning itemfinder on the bottom of your screen (an application of the pokewatch thingy) where you don't have to tap on it? I'd actually use it then.
60) Once I cut a bush down, I clearly have indicated that I have cut. Can that bush please stay cut down?
Long post, but that is about everything I have to say on that. I don't think any of my additions would throw the game out of balance, they are just small things that would incredibly increase the fairness/all around flow of the game.
Thanks for listening