Answer: GIRATINA
Explanation: Giratina as we originally saw it was only its Altered Forme, with its Origin Forme coming in Platinum.
Answer: RUNAWAY
Explanation: Originally, when pre-release information for Ruby and Sapphire was being released and we first got to know about Pokémon abilities, Poochyena's Run Away ability was mistranslated as "Can't Run".
Answer: DUSKULL
Explanation: Duskull's Ruby and D/P Pokédex entries both say that Duskull pursues prey until the break of dawn. More amusingly, they both describe it with the words "doggedly pursue", even though the rest of the entry is worded differently.
Answer: UMBREON
Explanation: Umbreon's Japanese name (literally "burakki") is officially romanized as "Blacky".
Answer: PHOEBE
Explanation: Phoebe's outfit is reminiscent of both Bellossom and Shaymin, which seems decidedly odd for somebody who trains Ghost Pokémon - Grass Pokémon are associated with life and fertility, after all.
Answer: MAGNEMITE
Explanation: We've seen Magnemite hovering in the anime (and in the game sprites) since the first generation, but only in the fourth generation got the move Magnet Rise that allows it to avoid Ground attacks.
Answer: BELLSPROUT
Explanation: Sprout Tower, despite being dedicated to Bellsprout and containing Bellsprout statues, does not contain wild Bellsprout, only wild Gastly and Rattata and Sage trainers with Bellsprout.
Answer: PICHU
Explanation: Many comment on how every generation includes a new "Pikachu-ripoff": first Pikachu itself, then Pichu in the second generation, Plusle and Minun in the third, and then Pachirisu in the fourth.
Answer: NINJASK
Explanation: Ninjask's Japanese name, "Tekkanin", could by some obscure train of thought probably unique to me be read as a corruption of "tech canine" (not as it's pronounced in Japanese, of course, but just how it's written).
Answer: AMPHY
Explanation: Amphy was sick in the original Gold, Silver and Crystal, and since HeartGold and SoulSilver are remakes, we now see Amphy being sick again.
Answer: PORYGON
Explanation: The answer is actually Porygon2, but because all non-alphabetic characters are stripped out of words that appear in the crossword, Porygon2 cannot appear because in the crossword it turns into just Porygon.
Answer: AARON
Explanation: Aaron's introduction when you battle him in D/P/Pt includes the declaration that he wants to be perfect (just like his Bug Pokémon).
Answer: OAKSLETTER
Explanation: Oak's Letter is the key item used to activate the in-game Shaymin event in Diamond, Pearl and Platinum.
Answer: SHAYMIN
Explanation: In the eleventh movie, Giratina and the Sky Warrior, Shaymin is convinced that Giratina wants to eat it.
Answer: PSYBEAM
Explanation: The flavor text for Psybeam in both the third and fourth generation describes it as "a peculiar ray".
Answer: AEROBLAST
Explanation: In Gold, there was no way to get a Lugia with Aeroblast, since the Lugia one caught in Whirl Islands was level 70 and had already forgotten it, and it was impossible to breed legendaries. In HeartGold and SoulSilver, however, Lugia learns Aeroblast at level 43, and when you capture it at level 70 in HeartGold, it knows Aeroblast, Punishment, Ancientpower and Safeguard - not even the Move Relearner is needed to get an Aeroblast Lugia in HeartGold.
Answer: HONCHKROW
Explanation: A skullless 7 across is dusk - take the "skull" out of Duskull, and you're left with the other word combined with it. When you add a rock (or rather, the word "stone") to that, you get a Dusk Stone. The five HG/SS fours (completely obscure, I know) refer to Karen's Murkrow: the fourth Elite Four member's fourth Pokémon, which is level 44. Thus, use a Dusk Stone on a Murkrow, and you get a Honchkrow.
Answer: MISMAGIUS
Explanation: According to its Pokédex classification, Mismagius is a "Magical" Pokémon.
Answer: ILLUMISE
Explanation: Illumise's name is derived from the word "Illuminate", but unlike Volbeat, Illumise does not have the Illuminate ability.
Answer: INFERNAPE
Explanation: Only Infernape and Deoxys give one effort point to each of Attack, Special Attack and Speed, the most important stats for a mixed sweeper.
Answer: RAREBONE
Explanation: When you go through Turnback Cave after capturing Giratina, the game counts how many rooms you passed through on your way, and when you get to Giratina's room, a prize will be waiting for you depending on how many rooms you went through. The "second prize" is a Rare Bone.
Answer: POISONJAB
Explanation: D. and L. P. are Discharge and Lava Plume, basically Electric and Fire's versions of Poison Jab, except that Poison Jab is a physical attack that makes direct contact.
Answer: FANTINA
Explanation: Fantina was demoted from the fifth Gym leader in D/P to the third in Platinum.
Answer: MAGICALLEAF
Explanation: Not a grassier version of Mismagius, but of the clue: it's a magical leaf.
Answer: LUCKYPUNCH
Explanation: The official romanization of Chansey's Japanese name is "Lucky", and the Lucky Punch raises Chansey's critical hit ratio, making it, well, luckier.
Answer: UTURN
Explanation: When Ingrain is in effect, the Pokémon cannot switch out or be Roared or Whirlwinded out of the arena. Baton Pass can be used, but then the effect is passed on to the Pokémon that is sent out afterwards. U-Turn, however, will allow the Pokémon to switch out and end the effect of Ingrain altogether.
Answer: CACOPHONY
Explanation: The ability Cacophony existed in the third-generation games' coding, but no Pokémon actually had it, and it was identical to the Soundproof ability. In the fourth-generation games, it was removed, since it was unnecessary.
Answer: SPROUTTOWER
Explanation: This refers to the POV shots of Sprout Tower in HeartGold and SoulSilver. In the morning, there is a Rattata on the floor; in the day, there is a Rattata up by the ceiling; and in the evening, there is a Gastly up by the ceiling.
Answer: HYDROCANNON
Explanation: Although the actual base power of Hydro Cannon is the same, it can only be taught to your Water-type starter, and Feraligatr - the Water-type starter in HG/SS - has the lowest Special Attack out of all the Water-type starters.
Answer: OREBURGHMINE
Explanation: When you first come to Oreburgh City, Roark is not in his Gym because he is down in the mine. He is the only first Gym leader who is not in his Gym when you first come to the city, so it could not be anyone else.
Answer: NASTYPLOT
Explanation: In Platinum (and HG/SS), some changes were made to Darkrai's moveset. While it could always get Ominous Wind by move tutor, Faint Attack and Nasty Plot were new. My excuse for Faint Attack not being a valid answer is that there is some sort of a pun on how Darkrai now gets the plot at last. Or something.
Answer: AGATHA
Explanation: Agatha trains Ghost-types, and she is no longer a member of the Elite Four in G/S/C (and HG/SS, naturally), having disappeared without a trace. While Lorelei is young and must have gone home to Four Island, Agatha was an old woman who could have died in the three-year-interval between the games.