Theme: MEWTWO
Answer: DRAGONITE
Explanation: Dragonite's appearance is commonly likened to Barney the Dinosaur, but Barney is purple. One can see the resemblance in the rest, though. Dragonite connects to the theme because it was a Dragonite that delivered the invitation to Ash in the first movie, which starred Mewtwo.
Answer: BLASTOISE
Explanation: Squirtle and Wartortle's names both stem from 'turtle' while Blastoise's comes from 'tortoise'. The Squirtle family resembles tortoises in appearance, but then again they ARE Water-types... It connects to the theme because Blastoise was one of Mewtwo's cloned Pokémon in the first movie.
Answer: WIGGLYTUFF
Explanation: Wigglytuff's Gold version Pokédex entry says that if two of them snuggle together, they don't want to be separated. Wigglytuff relates to the theme because it, like Mewtwo, has a W in its name. :P Hey, who said the words had to relate to the theme in some sensible way? At least, one of the trainers who got across the storm that Mewtwo created had a Wigglytuff, so we can pretend that's it.
Answer: DEWGONG
Explanation: Dugongs, Dewgong's namesake, are related to elephants, so one could assume this applies to the Pokémon as well... One of the trainers who crossed the storm to get to Mewtwo's island had a Dewgong.
Answer: ZAPDOS
Explanation: Bubble is Zapdos's 'numerical counterpart' among Pokémon attacks: Zapdos's National Pokédex number is 145 while move number 145 is Bubble. This is obviously kind of ironic as Bubble is a weak Water attack, and Zapdos is a powerful Electric Pokémon. Zapdos, like Mewtwo, is a Kanto legendary Pokémon that has played a part in a movie.
Answer: DISABLE
Explanation: Disable is the only move that all four of those Pokémon learn by level-up. It is also one of Mewtwo's starting moves.
Answer: MEOWTH
Explanation: 'Meowth' is nearly an anagram of 'Mewtwo' - all you need to do is change the h to a w, and you can rearrange the letters into 'Mewtwo'.
Answer: HYPNO
Explanation: Hypno is one of the Pokémon that show gender dimorphism in Diamond and Pearl - female Hypno have thicker fur around their neck than male Hypno. Hypno is a Psychic Pokémon like Mewtwo.
Answer: MEW
Explanation: Mewtwo is, as we all know, cloned from Mew.
Answer: NURSEJOY
Explanation: Isn't a word like 'Yay!' a sign of joy? :P She relates to the theme because Mewtwo kidnapped her in the first movie to be his servant.
Answer: VENUSAUR
Explanation: Its name is VENUSaur, after all. The team's name was changed to Team Galactic in the English version, but it does have Commanders by the names of Mars, Jupiter and Saturn. Venusaur was one of the Pokémon that Mewtwo cloned in the first movie.
Answer: PORYGON
Explanation: In Diamond and Pearl, Porygon2 evolves into Porygon-Z if traded while holding a "Dubious Disc". Porygon-Z looks rather possessed, and the name of the evolution item doesn't help. Porygon, like Mewtwo, is a man-made Pokémon.
Answer: KYOGRE
Explanation: Kyogre's ability Drizzle causes an automatic downpour, making it have more to do with rain than any other Pokémon. Like Mewtwo, Kyogre is an '00ber', a Pokémon banned from most ordinary competitive play due to its extreme power.
Answer: THUNDERWAVE
Explanation: Thunder Wave is TM73 in Diamond and Pearl, and Mewtwo can learn this TM.
Answer: PINSIR
Explanation: Pinsir's counterpart is Scyther, who got an evolution in Gold and Silver. Many people thought Pinsir should get an evolution in Diamond and Pearl to be a better counterpart to it, but even as a bunch of other Pokémon got evolutions, that didn't happen. Pinsir was one of the Pokémon owned by the pirate that Ash battled at the beginning of the first movie, which was of course about Mewtwo.
Answer: RECOVER
Explanation: The #377 refers not to Pokémon #377, but to move #377, Heal Block. This move prevents the target from using recovery moves (such as Recover) for five turns. It relates to the theme because Mewtwo learns Recover.
Answer: SPLASH
Explanation: This is slightly similar to 11 across: we are again talking about move counterparts to Pokémon. Mewtwo, the theme and according to the first movie the most powerful Pokémon that ever existed, is Pokémon number 150 - and oh-so-ironically, attack number 150 is none other than Splash, the only move in the game that does absolutely nothing.
Answer: MARILL
Explanation: Marill is a mouse and its silhouette, minus the arms, legs and tail, is scarily similar to Mickey Mouse's head. Oddly enough, I got multiple solutions guessing Raichu for this. o_O Marill's first appearance was in the Pikachu short before the first movie, which starred Mewtwo.
Answer: MACHAMP
Explanation: This clue is very, very bizarre, but it refers to 'Wii are the champions', a parody of Queen's 'We are the champions' that is about the (at the time the crossword was made) upcoming Wii console. Machamp's name is derived from 'macho' and 'champion'. It connects to the theme because one of the Pokémon that the pirate Ash fought at the beginning of the first movie (which was about Mewtwo) was Machamp.
Answer: METAGROSS
Explanation: It's MetaGROSS, after all (and yes, I know the "gross" part is actually referring to size). It connects to the theme because Metagross and Mewtwo are both Psychic Pokémon.
Answer: WOBBUFFET
Explanation: Wobbuffet is commonly used for capturing Latias and Latios in R/S, thanks to its Shadow Tag ability. Latias and Latios are often referred to collectively as Lati@s due to the @ character's resemblance to both a and o, and that is the point in this clue. Like Metagross, Wobbuffet connects to the theme because it's a Psychic Pokémon.
Answer: SAFFRONCITY
Explanation: Saffron is a spice. Saffron City was home to the most major Team Rocket takeover of Red, Blue and Yellow - Mewtwo's generation - and Mewtwo was of course created for Team Rocket.
Answer: GOLEM
Explanation: Okay, random clue, but basically Golem is rounded and learns Rollout, and its Crystal version Pokédex entry says that even dynamite can't scratch its hide. One can speculate that since it is round and can use Rollout, it could roll on the floor laughing its a** off... it it had one. o_O Golem was one of the Pokémon that the pirate Ash battles at the beginning of Mewtwo Strikes Back had.
Answer: VENOMOTH
Explanation: Venomoth is one of the Pokémon that is now, after the physical/special split of attacks in Diamond and Pearl, finally able to use its STAB attacks efficiently - its Special Attack is much higher than its Attack, and previously both Bug and Poison attacks were physical. Venomoth was one of the Pokémon that the pirate Ash battled at the beginning of Mewtwo Strikes Back had.
Answer: DEOXYS
Explanation: This clue refers to the first Pokémon Battle Revolution video, in which Pikachu and Groudon were seen battling Deoxys and Wailord. In the video, Pikachu was seen running up to Deoxys, jumping at it and physically striking it - a feature that Pokémon fans had been moaning for in the 3D games for years - and Groudon used a Hyper Beam on Deoxys that seemed to show destructable environments, another feature that got many excited. Both of those interesting attacks had Deoxys as their target, meaning people enjoyed seeing when Deoxys was hurt in that video (not because it was hurt, of course, but because of how it was being hurt). Deoxys relates to the theme because like Mewtwo, Deoxys is a legendary Psychic Pokémon that has been the star of a movie. Additionally, both of them are connected to the concept of DNA - Mewtwo has modified Mew DNA, while Deoxys literally is a DNA Pokémon according to the game.
Answer: BLISSEY
Explanation: Hey, they say ignorance is bliss. Blissey and Mewtwo have both had the honour of having the highest base for some particular stat in the game - Blissey for HP and Mewtwo for Special Attack.
Answer: ESPEON
Explanation: Espeon evolves from Eevee by happiness at day, but none of the Advance games had any such thing as day and night - the closest to it was the clock of R/S/E, so Eevee was forced to evolve into Espeon and Umbreon despite the lack of day and night. In Diamond and Pearl, the day and night system are back, and evolving Eevee into Espeon and Umbreon is no longer as awkward as it used to be. As for why it isn't Umbreon? Espeon is a Psychic-type like Mewtwo, while Umbreon has no connection to it.
Answer: NUGGETBRIDGE
Explanation: Nugget Bridge is a place where a Team Rocket member asks you to join the gang once you reach the end of it in Red, Blue, Yellow, FireRed and LeafGreen. He will also give you a Nugget - an item you can sell for 5000 Pokédollars and which he supposedly gives to anyone who can beat all the trainers on the bridge, so Team Rocket are clearly spending a whole bunch of unnecessary money on that. What's more, according to The Origin of Mewtwo, they were funding Professor Fuji's research for cloning Mewtwo as well. Giovanni's got to be pretty darn rich.
Answer: COINCASE
Explanation: Team Rocket runs the Celadon City Game Corner in Red, Blue and Yellow, where people pay oodles of money for game coins to fill their Coin Cases with. See above for the relation to Mewtwo.
Answer: CHARIZARD
Explanation: In Mewtwo Strikes Back, the Venusaur, Blastoise and Charizard that the surviving trainers brought to the island are made to battle Mewtwo's cloned versions. Out of the originals, only Ash's Charizard does not have a nickname.
Answer: CERULEANCAVE
Explanation: Cerulean Cave is also known as the Unknown Dungeon, and 'Dodge Unknown Nun' is an anagram of 'Unknown Dungeon'. Cerulean Cave is of course where Mewtwo is found in Red, Blue and Yellow.
Answer: UNOWN
Explanation: Those four words are the words that appear in the Unown Pokédex in G/S/C for the B, J, U and I Unown. Unown was the title character of a movie (Spell of the Unown) like Mewtwo.
Answer: GIOVANNI
Explanation: Giovanni has a Persian he is very fond of. He is also the man who commissioned the creation of Mewtwo and later abused Mewtwo's trust.
Answer: TELEPORT
Explanation: Mewtwo likes flying places instead of teleporting there for some reason. Well, perhaps it's no wonder: Mewtwo only learns Teleport as a R/B/Y TM.
Answer: DONPHAN
Explanation: Hey, it IS based on the elephant after all. Donphan was first shown in Mewtwo Strikes Back, as one of the Pokémon that the pirate Ash battles near the beginning owns.